To be more accurate:
* we use 2 installations in 2 differents directories: ~/ctf, ~/defrag
* in each directory we unzip the openarena archive
* we set up config files in each directory: baseoa for ctf and defrag for... defrag
The problem is that ~/.openarena is common to every running instance.
To keep things clean, we use 2 directories for our maps repository : ~/maps-defrag for defrag maps and ~/maps-ctf for ctf maps. Then we use unionfs to "union" ~/maps-defrag and ~/maps-ctf in ~/.openarena/baseoa.
You don't need to do that, but we like doing things the cleaner way.
The same way, instead of using "screen" command, you can do a clean init (/etc/init.d/openarena-ctf) script that launch your servers when the machine boot up.
Our configuration is more complicated but you better have to start with simple things.