Perhaps your best bet for Atomic 4 specific advice is over at the Moyer Marine forum: Moyer Marine Atomic 4 Community - Home of the Afourians - Powered by vBulletin
Very helpful group of people there who have done what you are intending to do and will freely give you good advice. That is not to say that you wont get good advice here but it is highly likely that most people here have diesel engines of one sort or another. Doing the engine alignment is the same whether diesel or gasoline powered though.
One of the first things you should do once you remove the old A4 is inspect the engine mounts carefully. Check for any rot or soft spots in any wood used to make the engine beds. The engine beds need to be firm and strong otherwise your engine is likely to go out of alignment.
If the engine beds are solid then it should be a straight swap. Alignment is done using precise shims that get inserted under the engine mounts. McMaster-Carr