Usually the biggest area of clearance issues is the back of the tranny. I find it easiest to get the tranny in the air. I do this by attaching rope to it and then going over the strut brace as a point of leverage. I tie it off, and voila, the tranny is elevated.

Once it is in the air you can maneuver it easier. I usually have to raise and lower the motor a few times until I get it to the "sweet spot" where I can get the tranny into place. Like Tim, once I get it into place I have someone thread the two top bolts on. From there, its cake.

1999 Eclipse GS
Built motor
Hahn 16G Turbo w/ FMIC
Hahn Stage 5 Portfueler (270's & 500's)
Zeitronix Zt-2 wideband w/ 3.5bar MAP
3" SS Turbo Back
CM Stage 4 Clutch and Fidanza Flywheel
Baer Big Brake Kit