The bolts? Aren't long enough for the toilet after laying tile. What do we do next?

Buy longer bolts and a new wax ring.

When we set a toilet we cut off the excess closet bolts. This will make them too short after tiling a bathroom floor. Purchasing regular closet bolts should solve your problem. Also if you're concerningt about the additional heigth causing a problem with the wax seal I would install a wax seal with a attached funnel. Just follow Skibergers advice and you'll be fine. Good luck, Tom