V- 8 alingnment

[johnny be good]

OK you guys help with the alingment tool specs.so this should be easy. I hate to sound stupid but most of the time little tricks from someone thats been there can save alot of time for the novice. After I rebuild my transom and reinstall my transom plate And have my new alingnment tool what is the best procedure to line up the engine. Should I have the tool in place and slide the engine with coupler onto it and shim while its still hanging in position ? If I set the engine back on its original markings and need to line it up how would you know if it needs to go up,down right or left?