a little bit of substrate will not hurt them. A trick we did when we used a substrate was put down paper towels and then feed on top of that. It worked really well. Eventually we switched to bins and now they are always on papertowels. It is really better for the snake and personally speaking I had less turn downs once I stopped feeding outside of the enclosure.

Also remember not to handle until 48 hours after feeding. This gives them time to digest.