Raising and lowering of the engine should be done evenly on both sides. Start off initially with the rear engine mounting screws tightened down, lift the front of the engine with a chain block, or similar (there should be a lifting ring attached to the thermostat housing for just this purpose), and run the side mount lower nuts up until their just touch the bottom of the mount. From here on, you move the lower nut on both sides the same. No exceptions.
The full method of checking the alignment is to check it at 90degree intervals. From this you can then determine which way the engine needs to go, up or down (there is no other option)....
If you find that the engine alignment appears to be slightly to one side, it means the transom thickness where the inner and outer transom plate are attached is uneven... Don't try to correct that by moving only one side mount adjusting nut, all you'll do is put stress on the rear mountings (but 'twisting' the engine slightly) and cause them to fail prematurely...
Chris....