Windows will basically create one large "virtual desktop" that is shared by both monitors. You can tell windows where the secondary monitor is in relation to the primary, and then simply move your mouse to and from the secondary monitor. For instance, if you place the secondary monitor to the right of your primary, you'd simply just move the mouse off the right side of the screen and the pointer would appear on the secondary monitor.
You can drag windows between monitors in the same fashion, or even split windows between the two monitors. It works fairly well. There are some weirdities, though. Depending on how a program saves its window locations, you might have to move windows around between monitors every time you start a session. For instance in n-Track if I move a VU meter to the secondary monitor, and then close and reopen n-Track, the VU meter appears back on the primary monitor. So, yes, some programs are more "dual monitor friendly", but all programs incorporating multiple windows can benefit from dual monitors....not to mention that it sure makes life easy when you're running several programs at once.
Now I've only done this in Windows 2000 and XP, and am not sure how well it works in 98 or ME. It does work very nicely in Win2k and XP. I simply installed a little PCI video card I had lying around (an old S3 Trio 2MB thing) and windows took care of the rest. In the "display settings" dialog you'll find everything you need to set your primary monitor, "extend your desktop" over the secondary monitor, and position your secondary monitor in relation to the primary. It's pretty slick.
Probably the oddest thing to get used to at first is that the BIOS will favor PCI over AGP so all the bootup and "loading windows" crap will appear on the secondary monitor...even if you disable the secondary monitor in windows. Some BIOS's have an option to set PCI or AGP as primary, but setting it to AGP sometimes yeilds bad results. Oh, and the reasons you'd disable the secondary monitor from time to time would be a) you want to play a game and the game freaks out when it tries to take over the display b) you want to save that last tiny bit of CPU power for a big ass mix that's really taxing the system. On 2K/XP, you can enable and disable the secondary monitor without rebooting so it's no big deal...I'm not sure about 98/ME though.
Slackmaster 2000