There's two schools of thought on this;
on a complete car, support it by the suspension points to simulate loads the car is used to seeing on the road and this prevents creating any problems with panel alignment. Downside is any wedge or uni-body deformation that has settled in to the chassis is now locked in to place.
Other thought is to support the uni-body in multiple locations creating a square and plumb situation, then lock it in to place with conenctors. Downside to this is your going to find it tough to square and now some panels may interfere with each other.