The proper way would be to plumb bob down from all the mounting points on the underside of the body and fix anything out of square or out of line.

Then measure all mounting points on the rear end and be sure they are equal at all attatchment points on both sides.

Agreed here. Most GM cars I have crawled under have about a 1/2" off-set in the drive shaft tunnel allowing for the rear pinion yoke to be about 1/2" off-set to the driver side.

If you are going to do any modifications to the rear end including suspension this is the time to center the drive-shaft and pinion yoke to the off-set possition (centered in the drive-shaft tunnel) then build every thing to the squared position. It typically ends up with 1/2" wider axel on the passenger side to compensate.

My 9" rear end set up has the drive-shaft and pinion yoke that are centered to the 1/2" off-set in the tunnel to one side and then my rear end axel is 1/2" longer on the passenger side (opposite side).

Square everything up to the frame and suspension mounting points, not the body lines. That way the importance is focused on the tire contact patch being true and square. Once the suspension is true, then you can adjust body panels for the proper look and proportions.

Sorry long 2cents here.

Ford did it too!!
 

I'm running a ford 9 inch from a 67-69 Mustang/Cougar in DETONATOR and it was offset to the drivers side. When I got the Chris Alston's weldment bracket for the two upper links for the g-link they actually had a set of index holes for 0" and 1/2" offsets. Of course mine was somewhere in the middle so the shop that welded up the brackets had to slot the hole between the offsets to get it dead nuts in the middle of the housing.