If I remember correctly, it's seta server1 "ip"... seta server16 "ip".  I never used it though, so maybe that doesn't work.  Also, if you launch q3 you're in baseq3, then connect to a server with a mod, you'd be in that mod, so if you drop back out to try to connect to a favourite, you'd not have the ones you set in baseq3/q3config.cfg.  You could make it a config in baseq3 that you could execute if you see they're not there.

I didn't see any difference after setting it up through "seta server".  I didn't think about just doing an executable config, though!