You can only select the folder layout on website creation. To change it you have to delete the website in the webconfig and recreate it. This is because your website will completely break if you change from one layout to another when the original site was working.

Anyway, for the sandboxed layout (which is the recommended one), your website should go into /var/www/virtual/<website>/html - see the DocumentRoot parameter in flex-80.conf (and also the documentation). With the Standard layout, /var/www/virtual/<website> is used.

I tried playing round with file ownership and it does not seem to matter. I thought the normal file ownership was apache:allusers and that there was a nightly cron job to change it, but I could be wrong.

Thanks for the reply. I am using the ClearOS Web Site set up from the webconfig. The default site works fine but not the other (dynamic DNS) ones. I am using Sanboxed Folder Layout. It won't let me change the folder layout. My index files are in the root directories of the website directories (/var/www/virtual/<website>/). Permissions for index.html files are -rwxrwxr--x <username> admin for one and -rw-rw-r-- <username> admin for the other two. I don't think I have a .htaccess file. I am certain I did not try to create one.

#----------------------------------------------------------------
# WARNING: This file is automatically created by webconfig.
#----------------------------------------------------------------


# Authentication mechanism
DefineExternalAuth pwauth pipe /usr/bin/pwauth
DefineExternalGroup pwauth pipe /usr/bin/unixgroup

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:80>
ServerName <URLnameofdefaultsite>
ServerAlias *.<URLnameofdefaultsite>
DocumentRoot /var/www/html
ErrorLog /var/log/httpd/error_log
CustomLog /var/log/httpd/access_log combined
</VirtualHost>

<Directory /var/www/html>
Options +Indexes +FollowSymLinks -IncludesNOExec
AllowOverride All
Require all granted
<FilesMatch \.php$>
SetHandler None
ForceType text/plain
SetHandler application/x-httpd-php-source
</FilesMatch>
</Directory>

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:80>
ServerName <URLnameofvirtualsite1>
ServerAlias*. <URLnameofvirtualsite1>
DocumentRoot /var/www/virtual/<URLnameofvirtualsite1>/html
ErrorLog /var/www/virtual/<URLnameofvirtualsite1>/logs/<URLnameofvirtualsite1>_error_log
CustomLog /var/www/virtual/<URLnameofvirtualsite1>/logs/<URLnameofvirtualsite1>_access_log combined
</VirtualHost>

<Directory /var/www/virtual/<URLnameofvirtualsite1>>
Options -Indexes +FollowSymLinks -IncludesNOExec
AllowOverride All
Require all granted
<FilesMatch \.php$>
SetHandler None
ForceType text/plain
SetHandler application/x-httpd-php-source
</FilesMatch>
</Directory>

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:80>
ServerName <URLnameofvirtualsite2>
ServerAlias *.<URLnameofvirtualsite2>
DocumentRoot /var/www/virtual/<URLnameofvirtualsite2>/html
ErrorLog /var/www/virtual/<URLnameofvirtualsite2>/logs/<URLnameofvirtualsite2>_error_log
CustomLog /var/www/virtual/<URLnameofvirtualsite2>/logs/<URLnameofvirtualsite2>_access_log combined
</VirtualHost>

<Directory /var/www/virtual/<URLnameofvirtualsite2>>
Options +Indexes +FollowSymLinks -IncludesNOExec
AllowOverride All
Require all granted
<FilesMatch \.php$>
SetHandler None
ForceType text/plain
SetHandler application/x-httpd-php-source
</FilesMatch>
</Directory>

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:80>
ServerName <URLnameofvirtualsite3>
ServerAlias *.<URLnameofvirtualsite3>
DocumentRoot /var/www/virtual/<URLnameofvirtualsite3>/html
ErrorLog /var/www/virtual/<URLnameofvirtualsite3>/logs/9-11.dnsalias.net_error_log
CustomLog /var/www/virtual/<URLnameofvirtualsite3>/logs/9-11.dnsalias.net_access_log combined
</VirtualHost>

<Directory /var/www/virtual/<URLnameofvirtualsite3>>
Options -Indexes -FollowSymLinks -IncludesNOExec
AllowOverride All
Require all granted
<FilesMatch \.php$>
SetHandler None
ForceType text/plain
SetHandler application/x-httpd-php-source
</FilesMatch>
</Directory>



#----------------------------------------------------------------
# WARNING: This file is automatically created by webconfig.
#----------------------------------------------------------------


# Authentication mechanism
DefineExternalAuth pwauth pipe /usr/bin/pwauth
DefineExternalGroup pwauth pipe /usr/bin/unixgroup

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:443>
ServerName <URLnameofdefaultsite>
ServerAlias *.<URLnameofdefaultsite>
DocumentRoot /var/www/html
ErrorLog /var/log/httpd/error_log
CustomLog /var/log/httpd/access_log combined
SSLEngine on
SSLCertificateFile /etc/pki/CA/sys-0-cert.pem
SSLCertificateKeyFile /etc/pki/CA/private/sys-0-key.pem
SSLCACertificateFile /etc/pki/CA/ca-cert.pem
# No weak export crypto allowed
SSLHonorCipherOrder on
SSLProtocol all -SSLv2 -SSLv3 -TLSv1
SSLCipherSuite ECDH+AESGCMH+AESGCM:ECDH+AES256H+AES256:ECDH+AES128H+AES:ECDH+3DESH+3DES:RSA+AESGCM:RSA+AES:RSA+3DES:!3DES:!aNULL:!MD5
SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown downgrade-1.0 force-response-1.0
</VirtualHost>

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:443>
ServerName <URLnameofvirtualsite1>
ServerAlias *.<URLnameofvirtualsite1>
DocumentRoot /var/www/virtual/<URLnameofvirtualsite1>/html
ErrorLog /var/www/virtual/<URLnameofvirtualsite1>/logs/<URLnameofvirtualsite1>_error_log
CustomLog /var/www/virtual/<URLnameofvirtualsite1>/logs/<URLnameofvirtualsite1>_access_log combined
SSLEngine on
SSLCertificateFile /etc/pki/CA/sys-0-cert.pem
SSLCertificateKeyFile /etc/pki/CA/private/sys-0-key.pem
SSLCACertificateFile /etc/pki/CA/ca-cert.pem
# No weak export crypto allowed
SSLHonorCipherOrder on
SSLProtocol all -SSLv2 -SSLv3 -TLSv1
SSLCipherSuite ECDH+AESGCMH+AESGCM:ECDH+AES256H+AES256:ECDH+AES128H+AES:ECDH+3DESH+3DES:RSA+AESGCM:RSA+AES:RSA+3DES:!3DES:!aNULL:!MD5
SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown downgrade-1.0 force-response-1.0
</VirtualHost>

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:443>
ServerName <URLnameofvirtualsite2>
ServerAlias *.<URLnameofvirtualsite2>
DocumentRoot /var/www/virtual/URLnameofvirtualsite2>/html
ErrorLog /var/www/virtual/<URLnameofvirtualsite2>/logs/<URLnameofvirtualsite2>_error_log
CustomLog /var/www/virtual/<URLnameofvirtualsite2>/logs/<URLnameofvirtualsite2>_access_log combined
SSLEngine on
SSLCertificateFile /etc/pki/CA/sys-0-cert.pem
SSLCertificateKeyFile /etc/pki/CA/private/sys-0-key.pem
SSLCACertificateFile /etc/pki/CA/ca-cert.pem
# No weak export crypto allowed
SSLHonorCipherOrder on
SSLProtocol all -SSLv2 -SSLv3 -TLSv1
SSLCipherSuite ECDH+AESGCMH+AESGCM:ECDH+AES256H+AES256:ECDH+AES128H+AES:ECDH+3DESH+3DES:RSA+AESGCM:RSA+AES:RSA+3DES:!3DES:!aNULL:!MD5
SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown downgrade-1.0 force-response-1.0
</VirtualHost>

# -----------------------------------------------#
# Web Site
# -----------------------------------------------#

<VirtualHost *:443>
ServerName <URLnameofvirtualsite3>
ServerAlias *.<URLnameofvirtualsite3>
DocumentRoot /var/www/virtual/<URLnameofvirtualsite3>/html
ErrorLog /var/www/virtual/<URLnameofvirtualsite3>/logs/<URLnameofvirtualsite3>_error_log
CustomLog /var/www/virtual/<URLnameofvirtualsite3>/logs/<URLnameofvirtualsite3>_access_log combined
SSLEngine on
SSLCertificateFile /etc/pki/CA/sys-0-cert.pem
SSLCertificateKeyFile /etc/pki/CA/private/sys-0-key.pem
SSLCACertificateFile /etc/pki/CA/ca-cert.pem
# No weak export crypto allowed
SSLHonorCipherOrder on
SSLProtocol all -SSLv2 -SSLv3 -TLSv1
SSLCipherSuite ECDH+AESGCMH+AESGCM:ECDH+AES256H+AES256:ECDH+AES128H+AES:ECDH+3DESH+3DES:RSA+AESGCM:RSA+AES:RSA+3DES:!3DES:!aNULL:!MD5
SetEnvIf User-Agent ".*MSIE.*" nokeepalive ssl-unclean-shutdown downgrade-1.0 force-response-1.0

Are you using the ClearOS Web Site set up from the webconfig? If so:
Are you loading to the default site or a subdomain?
Are you using the Sandboxed or Standard Folder Layout?
Where is your index file?
What are its permissions and ownership?
Can you post the contents of /etc/httpd/conf.d/flex-80.conf and /etc/httpd/conf.d/flex-443.conf?

[edit]
Do you have a .htaccess file, and, if so, what is its contents?

If you don't use the ClearOS Web Site set, what is in your web sites .conf file in /etc/httpd/conf.d?
[/edit]

Thanks for the reply. When I do that a "403 Forbindden" error message:

"Forbidden
You don't have permission to access / on this server."

Any ideas?

Reading the docs, if you have an index page, you do not want Show Indexes enabled.

Thanks for the reply. I had already set "Show Index" and I had already looked at the documentation.

Assuming you are using the ClearOS Website config, how have you set "Show Index"? Have a look at the documentation attached to the page? Having said that, the option does nothing for me, but mine is a legacy set up.

Thanks for the reply. It turns out my ISP was blocking the ports so I changed that but now when I go to my websites it doesn’t load index.html even though it is there as I can see it in the shared directory on the LAN. What appears looks like a directory listing with no files listed with “Index of /“ as the heading. How can I fix this?

Do you have anything like IDS/IPS or app-attack-detector running? You can see any ipset blocks (attack-detector and IPS) with:

for SET in `ipset list -name | egrep 'f2b|snort'` ; do ipset list $SET -output save | grep add | awk '{print $2 " "  $3}'; done

Are you using the Web Server app? If so is Accessibility still "All"?

Can you use a scanning site to see if port 80 (and possible 443) are open to the internet? You could use the Shields Up test at grc.com (but if you read the content be wary of the scaremongering)?

If you've changed any external router, have you set up any port forwarding and made sure its management ports are not listening on ports 80 and 443?

When you checked your dyn.com logs and said all is fine, do you mean that your dyn.com name resolves to your current WAN IP?