OK, not much info to work with so I'm going to make some assumptions.
Your best bet would be to use your better card in the AGP slot as your primary. I'd use an nvidia card of some flavor for this...probably an MX if you are using cpu-driven visuals like some plug-ins for winamp and whatnot, or something heavier like a GF2 GTS if you are using openGL or directx visuals.
Use the built-in functionality of windows 2000 to use a 2nd video card. This one should be your secondary and used to control your visuals, run your mixer or whatever you need to do on it. It should be your secondary because full screen things like visual displays like to pop into full-screen mode on the primary monitor. You might be able to fool with it but you'll have the best luck running your controls and such as secondary.
Here's one nugget I can give you: You can make this work with identical or unidentical graphics cards with one exception: because nvidia uses one driver for many cards, be sure your two nvidia cards are IDENTICAL. If this isn't possible, make sure that one of them is nvidia and one of a completely different manufacturer. I've had some ugly experiences trying to get two dissimilar nvidia cards to work in such a way.
Bottom line: Get a cheapo graphics card and a good graphics card...plug em into a windows 2000 computer and you're off to the races. Windows 2k help files are actually helpful in this topic so check em out.
I'm waaaay to rusty on Windows 9x to help you out on that one but I don't believe it has dual monitor support natively. You might have to come up with some dual-monitor video card for that one. Maybe one of the resident Matrox gurus around here can help you out.
What visual software you running anyway? And where's the party? And are you going to play any Infected Mushroom or GMS?