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Unbolt the old flange and place the new flange over the hole. Next, drive in any mounting bolts through the flange and into the floor. Wax rings come either plain or with a funneled inside edge. If the flange is not tight on the floor it may be necessary to remove the wax ring and try again. Tighten or replace the flange screws if necessary This step is tricky and may take several tries. Shimmy the toilet form side to side much like you did to remove the old toilet (see above). Be sure not to over-tighten these bolts too much or tank will crack. Tighten one side a bit, and then move on to the other side. In other words, tighten simultaneously as much as possible. Over-tightening can result in a cracked bowl. Get the right balance between sealed and too-tight. Tighten the basin bolts by hand. Do not over-tighten.
Replace the old flange around the drain opening with a new one. Fit a new wax ring around the bottom of the toilet bowl, just around its drainage hole. Ensure flange is tight to floor. Lift and place the toilet bowl over the anchor bolts protruding from the floor. Once the anchor bolts fit snugly inside the floor bolt openings, rock the bowl from side to side in order to create a seal on the toilet drainage hole. Insert the bolts through the tank and base, then tighten lightly by hand. Insert shims or other spacers underneath the toilet to make it level. Tighten the floor bolts gradually with an adjustable wrench until secure. Install the decorative caps over the floor bolts. Carefully fit the basin over the bowl, making sure the basin bolts fit inside the bowl. Reconnect the water line and turn on the water supply. Caulk around the base of the toilet to ensure a good seal.