Jeremy I placed the new tank where I wanted it then marked the top of the tank where the toilet sits. I then drilled a 3-1/2" hole and glued in the new threaded flange. The closet flange from the toilet screws through from the top of floor into the tank.Then the toilet goes back in as it came out.
The tank companies have all the parts you will need.
If you have the stock tank setup the new tank will also need a 1-1/2" hole drilled in the top for the vent pipe.
If you need I can get you a complete list of what I used.
Let me know
Bob