You MUST create two FAT32 primary partitions.
You will install each windows into a primary FAT32 partition. You can create up to four primary partitions on a single ide drive. It means that you can install up to four win9x/me into a single drive. YOU CANNOT USE dos/win9x/me fdisk for partitioning, because it only creates ONE FAT32 primary partition. Use partition magic, linux fdisk, or another decent partitioning tool. Forget ms fdisk!
Install The first win (on c drive.)
Install the free boot manager called Extended Operating System Loader (XOSL). You can find it at:
www.xosl.org
It will install itself on mbr. (It smashes PQ boot magic. Belive me).
I don't know, but I think that win9x/me must be in drive C. You cand hide the first partition, so the second will be the C. Install the second windows.
To boot the first windows: All partitions visible
To boot the second windows: Hide the first partition
If you try it, e-mail me.