Do you want the drive bootable or do you want all of DOS on the drive?
Most of the stuff that is installed as "DOS" is useless nowadays and a waste of drive space.
I don't see the point.
Making the drive bootable is easy....
Start with a windows 98SE boot disk.
boot with that disk
run Fdisk to create/delete partitions on your hard drive as necessary
reboot computer (leaving boot diskette in)
run format on your hard drive like this...
FORMAT C: /S /U
the "S" switch transfers the "system" to the hard drive making it bootable
the "u" switch performs an "unconditional" format which fills the drive with zeroes
(the "u" is not mandatory but I like to do it anyway)
then remove your boot disk and reboot the computer
Here's a link that shows how FDISK works....
http://www.perfectdrivers.com/howto/fdisk-format.html