Ok, what I did was simple:
sudo mkdir /cdrom
sudo mount /dev/cdrom /cdrom
sudo cp /cdrom/Quake3/baseq3/PAK0.PK3 /usr/local/games/quake3/baseq3/.
It's fairly easy to mount it manually as you can see above (you'll only have to do the mount command there).
I see what's wrong with the q3 install -- it's throwing errors because it's 64bit. I just ran it with --keep (which doesn't erase the temporary files unpacked) and manually copied the files over to the q3 dir:
sudo linux32 sh linuxq3apoint-1.32b-3.x86.run --keep
sudo cp setup.tmp/baseq3/* /usr/local/games/quake3/baseq3/.
sudo cp setup.tmp/bin/Linux/x86/* /usr/local/games/quake3/.
sudo chmod +x /usr/local/games/quake3/q3ded
If you are going to have other users running servers, you should probably make a group called q3admin and restrict permissions:
sudo groupadd q3admin
sudo chown -R root:q3admin /usr/local/games/quake3
sudo chmod -R o=r /usr/local/games/quake3
sudo usermod -a -G q3admin rnr
-R is recursive, root:q3admin is the user and group ownership, o=r is setting all "other" users to read only, and -a -G q3admin rnr adds rnr to the q3admin group as a secondary (you don't want to change the primary group here).
For setting up stuff, only use /usr/local/games/quake3 directory for files all servers should be able to access. For instance, if one server is going to be running rocket arena 3, you would not put it there, you would put it in the server's home directory ~/.q3a/arena. If all servers should have access to a custom map, say jjm.pk3, then you'd put it in /usr/local/games/quake3/baseq3. If you only have one user for all servers (which is fine as long as you don't need to allow ssh/ftp access to the server for other users), then you might as well keep them all in .q3a anyway.