There are a few threads on this topic, See
viewtopic.php?f=1&t=848#p6249 for a basic checklist, but it boils down to:
1) Get the drive powered somehow (probably externally, for a regular spinny-platter desktop drive) and physically connected to the IDE interface on the Jr-IDE, and the Jr-IDE properly connected as a sidecar.
2) The Jr-IDE should recognize the drive properly on startup (ie. list a reasonable device name)
3) Boot from something else (eg. a DOS boot or setup floppy) such that you can run fdisk, format, etc. commands just as you normally would to create and format a bootable DOS partition on an empty drive.
minor mysteries and their solutions show up in that thread I linked, and others, but that's the gist. After step 1 and 2, it's just like any other drive, which of course is the beauty of the thing . . .
Personally the only thing that tripped me up (I'm using a CF adapter and card) a little were getting the bootsector fully cleared on the card (I had to use DEBUG to zero it, FDISK /MBR wouldn't do the job) such that I could create a primary partition w/ fdisk, and then later since I wanted to run DOS 5.0, manually patching the bootsector (again using DEBUG), as the PATCHDOS utility didn't work on this device, for whatever reason.
Instructions for those steps are here:
viewtopic.php?f=1&t=738#p5488
and here:
viewtopic.php?f=3&t=224
but you may not need them. I'd suggest reading through all 3 of the threads I've linked and see if that doesn't get you through . . .