Hi Alex
You said you have two B2D folders.
So, on the drive(s) where you want to store the B2D files, you have 2 distinct folders.
And, in BE "Devices", you have created 2 distinct 'Backup-to-Disk Folders', one pointing to each of the 'physical' folders.
(Check this carefully; BE records a 'default' and you may have ended up with 2 B2D Folders in BE, but both pointing to the same 'physical' folder on disk.)
Now, you have 2 distinct backup jobs.
In job setup, under "Device and Media | Device:" you have these two jobs pointing to the two distinct B2D Folders.
All should work fine.
Cheers