Yes, you indeed have to take away the RT-AC3100.

I have always used option 2 of what Nick suggested. In my situation it always worked fine.

I checked the Asus website for you, and you can set the AiMesh routers in accesspoint mode.

Here the link to the Asus site

This is going to be a generalisation as I don't use your router. There are normally two ways of using a router as a WAP on your LAN.
1 - Connect the router WAN port to your ClearOS LAN. In this mode you need to make sure the router LAN and ClearOS LAN are on different subnets. Keep the router DHCP enabled.
2 - Give your router LAN an IP address on the ClearOS LAN and disable its DHCP server. Connect the Router LAN to the ClearOS LAN. Do not use the router WAN.

1 has the advantage of being easier to set up, but everything on the router LAN is double-NAT'd and all devices on it will just appear as the router WAN IP to ClearOS, so filtering tools in ClearOS on anything on the router LAN won't work, or, at least, will apply to all devices on the router LAN. Devices on the ClearOS LAN will not be able to initiate a connection to any devices on the router LAN and sharing of LAN printers may not work.

2 is the more ideal set up in most scenarios. It avoids double-NAT and any wireless device appears to ClearOS as any wired device would. If your AI Mesh technology works in this scenario, it is the one to go for.