Grab the stock bump stop and with a lot of force wiggle it back and forth while pulling down, it will come out. After the bump stop is removed, use a 15mm socket and unbolt the bump stop cup and install the BB spacer. I like to use the stock 1/2" rubber spacer ubder the BB spacer in the front as most TJ's will have some front spring sag and this will help compensate for it. Then reinstall the bump stop cup and install new longer bump stops if your lift kit came with them.
Same procedure for fronts and rears. If you are replacing the rear shocks be very cautious with upper rear shock bolts if you live in the rust belt. They break very easily, and the gas tank is plastic, so it will not resist any torch heat at all.