I wouldn't worry about a little substrate -remember, they digest bone. But it's awesome that you're showing so much concern for him. That said, there's no reason to feed your little one anywhere but in his enclosure. Finally - are you feeding mouse or rat fuzzies? The reason I ask is that, generally, mouse fuzzies are WAY too small for a 2 month old BP.
Congrats on your adoption, though! And the start of an addiction...