It's going to be DOS. Will be using the SD card for my bridgeboard hard drive.
Not sure if I understand correctly, think I'm getting lost on this thread.
But to clarify, you're trying to prep the device with two cards:
1 - a CF card (presumably formatted with FFS) for your Amiga partition
2 - an SD card formatted as FAT/FAT32/"FAT95" for your DOS partition
Correct?
I would take it a step back and make sure the CF card is working 100% before trying to add another card.
For the FAT95/DOS partition I've never had any luck prepping them through HDToolbox; easier to just create a Mountlist/DOSDriver entry on your Miggy and format the card on a PC, that's what I do. Then I can interchangeably pop it out of my Amiga and into the card reader on my PC to transfer files. I still use it often enough that I sometimes forget that my Amiga has USB, too.