How much RAM do you have? I have a similar HD setup with an Atlas 10k, an Atlas 10k2, and 512MB RAM. I use my 10k2 for the OS's and I use the 10k for the swap. The 10k is so loud I can hear reads/writes. Anyway, I haven't noticed a difference because the swap file is rarely accessed. I'm probably gonna move it back over to the 10k2 so I can use the 10k for data storage or for another machine.
As for an ME/NT/2K installation, install in that order. With NT/ME in the mix though, the boot partition has to be FAT. ME can't read NTFS, NT can't read FAT32. I wouldn't install any of the OS's on a FAT partition just for capacity and performance reason. So my setup on just one 15K drive would be....
C:<1GB FAT for boot/swap
D: FAT32 WindowsME
E: NTFS or FAT32 Windows2k
F: NTFS WindowsNT (just guessing you'd use this least)
This way windows ME won't get screwy if drive letters change. You don't have to do this but it causes least complications. Ideally you would put the OS you use most in D:, E: 2nd most, F: least, but things can get screwy and it could be more difficult to install. I really recommend just losing NT so you can just do C: FAT32 WindowsME, D: FAT32 Windows2000 (or losing ME so you can do C: NTFS 2000, D: NTFS NT). Either of these two latter setups would let you experiment the 10k drive to use just for a swap file to see how performance changes. My guess is you won't see a difference.