Get better bolts. Replace them everytime. You'll have to cut them down with a hack saw. They have many different bolts. But a decent set will have a retaining washer. Either plastic or another nut and washer. You set those onto the flange and then they don't move around. The second set of nuts is then used to bolt the toilet down.

Alternatively you can try a neoprene or rubber gasket as you will not have to deal with the messy wax. Just make sure you always clean both sides of the flange and base of the toilet for a positive seal. Wax is tried and true for me but in this case a rubber gasket would be warranted.