I would slide the rear end into the car and center the pinion yoke in the tranny tunnel and go from there on the axle tube lengths needed to make your old or new wheels fit into your car properly
I think my truck rear end axle tube on the passenger side was 3/4 shorter than the left when I was all done with it
BTW, my axles extended past the splines in both spools into the center of the spools
I figure that way didn't hurt anything and I knew I had max spline engagement on both the axles and spool splines