i have found it works out the best if you can get your mototr in first. i have seen guys mess up nice paint jobs by leaning over the fenders installing an engine and fender covers seem to do more damage then they protect against.
I agree, just do your body work in the engine compartment and then repair the engine/drivetrain.The rest of the body work can be done at your leisure. If the car is mobile then you can take it wherever you may need to. I`m bad about scratching up things so that`s my angle on it. In a perfect world it probably would be best to do all the body work/paint and drop your new engine in the fresh car without as much as a scratch, (just like on T.V.).