Not sure how you would control a live rodent but for my redtail boa, I feed her fresh killed and I just hang it in front of her face and she grabs it, then I hold the tail and use a big shallow casserole type ceramic dish and plop her rat down in that and then shove her upper half of her body in there. Definitely not the norm but my red tail is so used to me that I could pick her completely up and she would continue to eat. I'm hoping to "train" the bp into the same style feeding but since she is so new, I use paper towels as my substrate and just watch her so she doesn't get the paper towel wrapped up with the rat since eating a paper towel can easily kill a snake from the impaction.
Also if you are using something like finely shredded aspen or eco earth I wouldn't worry. Now if you are using something like Reptibark which is pretty "chunky" and has big pieces, ingesting a bunch of those might be a problem. But you also got to remember, in the wild they ingest all sorts of stuff with their prey. Ours aren't wild but their bodies still function the same when it comes to ingesting a piece or 2 of substrate.