If you already have the shocks, bolt them into the top mount. Then jack up the jeep so its at full droop. Fully extend the shocks, then compress them about an inch or inch and a half. That little bit of compression helps if you come off the ground. A spring can overextend for a moment and this keeps the shock from doing the same. That's where the mount should go. At least that's what everyone has told me, and it worked for me too.
The ideal way would be putting on mounts where you want them, then ordering shocks to fit.
92 YJ, 4.0, 5" BDS springs, 1" booms, 1" BL, 35x12.50x15 MTZ's, Ford 8.8 with LSD, 4.10 gears. It's never done though.