Don't sweat it, it's really easy. You take the original Winamp group, copy it to a group using the name to the other exe and directory (I use "winampbad" for the bathroom and "winampkev" for my son Kevin's room, for instance). Then you set the group target to the correct Winamp and just learn it the codes from the remote you want to use for that Zone. About 20 minutes per zone, tops.
I got a more advanced system with Girder registers opening playlists (for instance if I press 666 on the remote, I get Mercyful Fate's brilliant "Don't Break the Oath" CD). This takes me about 40 minutes to program fully when I add another zone. I will add one in a few weeks, there's still room for two more soundcards in my pc - I'm using an Audigy Platinum EX for the Home Theater and Living Room zones, a Live of some sort or another for the bathroom, the internal C-Media soundcard of the mobo for the bedroom and an Aopen soundcard for my son's room. The next room that needs it's own zone (I laid the cable for it today) is the guest room. Believe me, this is something I enjoy doing after working with translation all day!