I was always told just the opposite, very first step was to center your rear wheel with the backbone of your frame. Lay your tire and wheel flat on the floor, put a straightedge across the tire, measure from the floor up to the straightedge, then place a piece of masking tire on the tire and mark a line with a pen in the exact center. Now mount your tire and wheel in your frame with no axle spacers in place. Next is to tape a piece of string in the center of your neck stem and run the string right down the center of your backbone and slide your wheel left or right so the mark you previously made on your tire is straight with the center of your backbone. Now that your wheel is centered, I usually adjust the rear belt pulley or sprocket so that the chain or belt will just clear the tire. This is done with pulley or sprocket spacers if needed. Now move to the transmission, it can be moved left to right with an offset trans plate or if just a little is needed to align your sprockets, use an offset sprocket. Now to the motor, which you know cant be moved left or right, you will use shims or offset sprockets or pulley if running a belt drive.
Im sure this is different than the way some people do it, but years ago I had a dude that had built several bikes tell me to start by centering the rear wheel first, then move forward from their. Hope this helps a little and I didnt confuse you too bad.