Insert the PowerQuests Boot Magic Dos boot disk you made & boot your machine
You'll be giving the option of which Primary Partition you want to boot to

Choose #1 ( & enter)

Have your OS's (Operating System) boot floppy ready & insert it after you've selected the Primary Partition
*NOTE*
If your machines supports booting from a CD Rom - most do these days - insert it and use that instead of floppies ( you may need to enter your BIOS to enable it, read your motherboards manual to learn how )

Install the OS as usual

If you already had a OS installed, it'd be on the 1st Primary Partition so choose #2
A special mention here...
I've noticed on some machines after using PowerQuest's Partition Magic Win2000/XP recognises the NTFS partition created but doesn't like to install to it, it want's to re-format the partition for itself, that's fine, go ahead & do it, but take particular notice of which partition you're selecting because the 2000/XP install will show you ALL the partitions on your Hard-Drive, be sure to select the right one
If you do happen to make a mistake & choose the 1st *Primary Partition*, all is not lost because you'd backed up all your important data before...didn't you???

Now if you're going the install of both OS's path, after you've installed the 1st one & it's up & running, re-boot using the PowerQuest's Boot Magic boot disk, select the 2nd Primary Partition, re-boot your machine & install the 2nd OS as usual

When both OS's are installed & running, you'll want to be able to select which one you want during boot up without needing to always use the BM boot disk, so now install theWindows version of PowerQuest's Boot Magic program on your Win 9x OS
When BM's installed & you run it for the 1st time, it should find your Win 2000/XP partition & add it automatically, don't sweat it if it doesn't though, just click on ADD, browse to the partition & select it, close BM and re-boot your machine, both OS's should now be visible and you can select which ever you want

If you've been playing around with Norton's Ghost and would prefer to go that route, I found a tutorial here