I can't see straight, so to make sure my sprockets are aligned and parallel, I use a length of stainless square rod clamped flat against the sprockets to make sure they're aligned and sitting parallel to the frame.
I also like to use a chain tensioner, since chain stretches unevenly throughout it's length...this compensates for the chain tightening and loosening as the sprocket turns.
On higher HP engines that like to move backwards on the mounting plate, I weld on two adjustment screws/nuts that push against the base of the engine, allowing me to adjust it for tension and tighten down without the engine shifting around on the plate. The dual screws allow me to ensure the engine stays parallel to the frame.
If I have a bike that won't allow me to have the wheels centered in the frame without the engine being severely offset from center, I'll add a jackshaft to get everything aligned and balanced.