rigging my new boat with 6s. one motor is staggered. I'm getting ready to align the transmissions and motors. it there a special tool for the rear motor/trans alignment? And how do you go about lining up the front motor and trans, where it will be connected on a driveshaft thanks for the input...

Yes Mercury has an alignment tool for the plug in. The process varies depending on what transom assy you have.
forward engine driveshaft hubs need to be parallel with each other, the engine hub must be slightly higher to give you between 1/2-3 degree slope on driveshaft. But remember hubs have to be parallel, so you don't get a compound angle. Mercury has install manuals also.