I usually do this on lifts, but have done it in my garage once as well.
In short, lower the car/motor and raise the car off of it. More detail here:
Disassemble everything to take the motor out(99%), but leave the two top motor mounts in place. This includes taking down the rear crossbeam(#1 in the diagram below) and the
passenger side beam(#4 in the diagram below) that bolt to the chassis(what your control arms mount to). Your lower control arms will already be be down, leave the top control arm in place, and leave the shock mounted top and bottom(take out the swaybar earlier, but put the link or a proper sized bolt back in place). All this will allow enough space for the motor to clear when raising the chassis. This will all swing out of the way when you are raising the car. You need people to help spot and pull stuff out of the way as you slowly/incrementally raise the chassis up.
Drop the car down until the motor/trans are sitting on a dolly(Put some wood below the tranny(on the dolly) to level it out with the oil pan on the dolly, adjust to the right spot when lowering the car/motor/tranny onto the dolly). Once the engine/tranny are fully set down on the dolly, take the two motor mounts off from the top, and begin raising the car slowly while watching to make sure everything is clearing, to make sure nothing is snagging, and to make sure you didn't forget to disconnect anything.
I use two SUV/large jack stands(with locking pins) on the rear most jack points to keep the rear of the chassis much higher than standard jack stands. I think I may have needed to have the front wheels on 2x12's to raise the front a little(or could have been on dolly's as well). This will let you roll the motor out without much worry of clearing.
Like Shawn, this is off the top of my head, but should give you the general idea. Use your common sense if I left anything out.
- - - Updated - - -
1