I have done it with an auto and a standard. Works fine with the auto, its just heavier and is scary looking when hanging in the air. You want to set your hoist so the tranny tips down as you lift the engine. It works best if you have a dolly on your hoist or you can push the car back. I lift the engine till the tranny hits the bellhousing and push the car back till the pan hits the front crossmember(hood, radiator and supports removed). Lift again, push the car back a little more. keep doing this till the tranny clears the bellhousing, lift the whole shebang over the front crossmember and push the car out of the way.

You can leave everything on the engine including manifolds, particularly if you are not worried about scratching the paint on the donor car.

I have heard you can also support the engine undo the crossmember and then lower the engine/crossmember to the ground. Not great if you want to be able to roll the shell away though.