Scott, like Steve, I've never heard of installing a toilet by screwing it down. That's not to say that there aren't some out there that are designed that way. Johns idea will get you past the flange but I feel that either your missing something or some thing is missing to do this project properly. In your case, I would think that the bolts should have been installed before the flange was secured to the floor. One suggestion, if you want to continue to install it the way you are, is to mark the holes with a pencil, remove the toilet, drill the pilot holes and reinstall the commode. Another suggestion would be to talk to your supplier. I've told my suppliers what I wanted to do, they've told me what I needed and how to do it. If I run into problems, I call them. They normally have the answers. This doesn't necessarly work at discount type stores but does at plumbing supply and Electrical supply houses. They can keep you out of trouble and be an immense help. Sure hope you get it installed soon.