I don't know if it really is necessary, but I start by adding two balls of fondant on the back. I think this helps when you lie him face side up to dry as it pushes the cheeks up and out. The main cheek volume is achieved another way.
Once again we're going to do a bit of plastic surgery on Thomas. This takes a bit of patience, but you'll get it. Remember that working with fondant is somewhat like working with play dough, not exactly, but somewhat. You'll be able to use your fingers to gently smooth the open checks over the inserted ball. Just gently use your index fingers to pull and rub the fondant down. If you have any bumps or uneven shapes, just lightly massage the fondant until it smoothes out.