Typically, on a backhalf, big tire, stock front clip car, the rear U-joint ends up being higher than the front joint, because the rear is substantially higher in the car than when the car was stock. Also typically on stock mounts, the engine/trans centerline is running downhill (towards the rear) about 3 degrees.
Pinion angle (or rear U-joint operating angle) on a drag car should always be negative,never positive. On this backhalf car example, this typically results in the pinion running downhill towards the front of the car. It also results in what is called a "broken back" configuration with the driveshaft being level or running slightly up towards the rear end.
I will usually try to move the rear of the trans some and work with the pinion angle to minimize the angles and the front to rear differences, but short of moving the engine, it's all just a compromise. Putting the engine where you want it fixes all of this.