Each USB drive HAS to be connected as the same drive letter every time that you connect it, and each must have it's OWN drive letter
Each drive should have a Backup2Disk on Removable Media folder defined on it.
Once that is set up, yes you can point your Monday job to the Monday drive, Tuesday job to the Tuesday drive etc.
You do not need to create a separate folder for each server. Think of the B2D folder as a tape drive and each BKF file as a tape volume. You can put as large a backup set on the drive as you wish, and can place as many backup sets in the folder as space permits.
Can't help you with the IDR question. IMNSHO that option is a piece of crap and I avoid it at all costs.