If you are referring to washers on the through bolt for the secondary, those control end freeplay and should not be used for alignment. If you have washers behind the secondary, you will have problems as they will destroy the seal over time. The secondary is designed to thrust against a certain area on the seal, and washers tend to contact a different spot. I would move the engine until the alignment tool just touches, while verifying Center-to-Center. You can also check belt deflection for fine tuning.