Once the bowl is in place, you can sit and straddle it facing the wall. Rock back and forth to compress the wax and seat the bowl. Use a level to make sure the bowl is level from front to back and left to right. Once it is properly seated, place the washers over the bolts and tighten the nuts. Caution: Over tightening the flange bolts will cause the bowl to crack and this cannot be repaired. Tighten the bolts just enough to secure the bowl in place. Do not tighten the bolts as a way to compress the wax seal.
Place the tank onto the bowl. If there were rubber spacers or tank bolt washers under the tank, be sure to replace them now. Note: You might want to take advantage of this opportunity to replace the gasket between the tank and bowl to prevent a future leak.
Place the tank washers over the bolts and insert the tank bolts down through the bottom of the tank. Place a washer on the bolt under the tank and then tighten the nut. Caution: Over tightening the tank bolts will cause the bowl or tank to crack and this cannot be repaired. Tighten the bolts just enough to secure the the tank to the bowl and to seal any leakage from the tank.
Reconnect the water line and turn on the water. Replace the tank cover. Inspect the water line, tank bolts and tank gasket for leaks. Once the tank is full, flush the toilet and check again for leaks, this time also checking the floor for leakage from the wax ring.
You may wish to caulk the joint between the bowl and the floor. This step is not required but it will keep the dirt from embedding in the putty and has a neater appearance.