The song I’m trying to create is in 4/4 but I need it to be looped at 5 and a half bars before the loop repeats. I need to do this so I can sync the rhythm and base loop from the Aeros properly. Is there a way to do this in the BB manager?
Do the song in 2/4.
I agree to this.
I’d say no. At least I gave up and modified the midi files in a proper midi editor 
So I exported the midi files, modified them and then imported back to BB Manager.
Personally I use Aria Maestosa
I do my midis in Logic Pro. The time signature transfers with the file. I would guess that other third party midi editors work similarly. I never use BB Manager for midi editing.
Having written songs with “oddities” that BB typically doesn’t like, I usually edit my beats to go for an entire verse/section per BB part but that does rob me of accessing fills. I often make the parts pretty varied from a dynamics standpoint, so I’m not missing much.