TMFAP is the severed arm of MIKE, sort of his vestigial evil side. BOB was MIKE’s familiar, when MIKE was still a murderer. He’d rape and murder to harvest pain and suffering, then bring it back to MIKE for consumption.
 
TMFAP and BOB have a conflict over pain and suffering that the latter owes the former–garmonbozia, it’s called–which is why TMFAP helps Cooper in his initial investigation into Laura Palmer’s death.
 
Half of this is just speculation. Twin Peaks is too abstract for any singular, objective interpretation of its lore.

Where we’re from the birds sing a pretty song, and there’s always music in the air.
 
Quite literally, in most cases here.