I have done it both ways. But either way dropping the rear of the engine as far as possible helps a lot. The bottom of the engine will stop on the cross support (or if a remember correctly you may need to place a shim under the engine to keep the sharp corner of the block from resting on the steering center link). I have also loosened the engine mounts first. Keep an eye out for the clearance between the fan blade and radiator, it should be fine. With it dropped like this it is much easier to access the top bolts using the long extensions Don recommend.
The only problem I had with removing and installing the transmission separate from the bell housing is when getting it back on. Trying to position the trans, while engaging the clutch arm, keeping the spring around the post, and bearing were difficult (for the 4 spd trans).