For now I'd suggest using an out-of-game browser if you're not already.
http://www.udpsoft.com/eye/ is a good free one, and it's not owned by the evil gamespy empire so that's a bonus.
Just manually point the Quake 2 game to c:\blahblahblah\paintball2.exe and open up Paintball underneath Other in the hierarchy tree on the left and press F5.
Or you can setup a custom command line for pball to use paintball2.exe while still using the regular Quake 2 exe for other q2 mods, but I'm assuming that if you don't use an out-of-game browser already then you don't have Quake 2.