Yes you can have a multi-server setup - to do this you choose "expert" mode during installation of ISPConfig3.
When asked if you want to configure mail you select "n" for no.
You will not be able to limit bandwidth or set up mail accounts through the ISP3 control panel though (there might be a way to do this depending on your setup).
Again, with the multi-server setup you can have a separate mysql database server and join the server to an existing ISPConfig3 server (or a seperate mail and ftp server(s) or as many web server nodes as you need too)
The servers communicate with each other through the master server.
Yes there are quite a few how-to's about setting up ProFTPd with ISPConfig3 - I use pureftp with TLS but have set up ProFTPd before.