You would change out the "doughnuts" on a TJ by doing something like this..
1. Loosen all 11 body mounts but leave the bolts in place.
2. Starting with one side, remove the 3 side body mount bolts and lower rubber bushings. Jack up the body using a floor jack and a block of wood under the tub or rocker protection. Raise the body up enough to remove the top rubber bushings.
3. Install new rubber bushings. Lower the body down on the rubber bushings making sure all bushings are seated correctly.
4. Install the bushing bolts but do not tighten.
6. Go to the opposite side, then front and rear and repeat steps 2 through 4.
7. Once all the rubber bushings have been replaced and correctly aligned, tighten all bols to factory torque specs.