To set the bowl onto the floor as well as onto its gasket, rock it carefully from front to back and side to side while pushing down hard. You can rotate it a few degrees each way, too. This forces out the excess wax. As the bowl meets the floor, make sure it is level and square with the rear wall. Don't raise the bowl from the floor while making adjustments, or you'll have to go through the setting process all over again and replace the waxing.
Drop washers over the hold-down bolts and thread on the brass nuts.
Using a wrench at this point can break the bowl. Re-check boths for tightness after several days of use. If the bowl has front-mounting holes, install two toilet studs with washers and nuts into the floor for the front two holes. If the toilet tank hardware comes separately, install it. Remember that the trip lever nut pro bably has left-hand threads.