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I've been leaning towards the idea of painting it with the whole car together, doing the engine bay/under hood, trunk, door jams first, then comming back later and doing the body. I think I would have a lot tougher time putting everything together without damaging something, not to mention chipping up the paint on all the bolts for the hood, doors, trunk, etc. But I'm sure the pros have their ways around that too. The door jams and trunk I'm not as concerned about, but would you mask off the engine bay after it's painted to prevent getting overspray when going back to paint the body?

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Yes definately use something to protect it. I used a roll of thin painters plastic used by housepainters from lowes (or home depot) its very cheap and usefull for other things as well. The clear especially floats around for while in the air just waiting for a place to stick where it shouldn't. As far as doing the jambs first I actually added a stripe similar to the factory billboards after the car was already painted, with doors on for alignment of the stripe and masked the inside of the doors and jamb so no overspray would get in thier.