Back in the day when win95 came out, everyone was trying the whole 'dual-boot' idea. And when the bootloader got corrupted, which inevitably happened, people dropped the whole idea. VMs brought back the whole concept in a different way. Personally, I always used the separate HD method as it way always easier.

I actually had one of my systems boot off of one drive and have DOS and Win31 installed on D:. Works fine. The only reason I had to do it this way was because SCSI drives were seen in the order of their SCSI IDs and I couldn't change the first drive ID (Seagate 157N).

Malik wrote:

The easiest way, if you have a floppy drive, is to create or use a MS-DOS 6.22 Floppy Bootdisk. When it boots, it will "see" the […]
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The easiest way, if you have a floppy drive, is to create or use a MS-DOS 6.22 Floppy Bootdisk. When it boots, it will "see" the FAT16 partition as the only accessible partition and will automatically assign it as C drive.
You can then either install MS-DOS 6.22 to the now "C" drive, or use the SYS command to transfer system files from the bootdisk to the now "C" drive, and copy the DOS files to the hard disk on your own. And while using the boot disk, use FDISK to select this E drive to Set as the Active Partition. The next time you boot, it will directly take you into this new "C" drive.
To go back to Windows98SE or XP, from the FDISK, choose the respective partition again to be Set Active.

The other method is to use a boot manager. I really like Smart Boot Manager, but it may not work properly on newer systems. The other one that I use a lot is PLOP boot manager. Smart Boot Manager is slightly easier to use. If you want to play safe, you can use a boot manager installed onto a floppy and use it to select the boot partiton. It will save the boot info directly on the floppy and not on the hard drive, and will leave the HDD alone.

And yet, one more method is to use the FDISK program while running a certain partition to set the active partition to another one.

This is exactly what I would try. Very simple since this is all native DOS. Fdisk was designed to change the active partition too, so you can simply use that when wanting to boot to a certain os. Just be careful about using older fdisks with modern partitions as it may not understand the table structure completely. Just be sure to use the fdisk from something like ME or freedos.

You need to buy BootIt BM. It'll do everything you want and more. I use it on most of my PC's and it is very powerful.
http://www.terabyteunlimited.com/bootit-bare-metal.htm

I can also recommend their backup suite with IfW, IfL or IfD. All work great and have been using it to backup my PC's of every flavor for years.