It depends on the level or height of the engine transmission combo in relation to the height of the rear end companion flange. I actually use the height of the rear axle center line as opposed to the companion flange and adjust for the distance that the pinion is below that line.
The pinion angle will effect the final driveshaft angle somewhat. If you're starting from scratch and can do it, try to set your power plant assembly angled slightly downward from the front to the rear. A slight rearward angle is almost always best.
Chassis Engineering has a lot of available information on this in their chassis set-up instructions.
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