|It's probably best to get a floppy drive.|
Fdisk won't allow more than one active partition. If C: is active and you want D: also active, the easiest way is to temporarily set C:'s drive type to NONE in cmos/bios setup. Then boot with floppy and run fdisk. Fdisk sees only one drive and you can then set its partition active.
You can switch between the two drives in cmos/bios setup, setting whichever one you don't want to boot from as NONE. Or, if both are enabled in cmos, the one connected to primary master will boot.
If you don't want to get a floppy drive you might try downloading AEFDISK:
I've never used it in the way you intend but I think it'll allow you to create more than one active partition.