If you read that thread you alluded to closely, you'll see where I was asked that same question... With my Bowtechs, I know they're going to perform best with the arrow at a 90-degree to the string. I start right there, and if I need to fine-tune it from there, I use the rest's adjustments.

You can get where you can set up a bow really quick like this, and if for some reason you don't get close where you start out at with tying your nocksets, you can quickly strip the string down and start over closer to where you need to be before fine-tuning with the rest.

The nice thing about having your nock sets tied in is the ability to cut off and re-ty new d-loops at will, fine-tuning their length as necessary -- and not having to start over from scratch to find your tune again. Just last night, I was playing with some different length d-loops on my 3d rig, and I tied three in quick succession knowing I wasn't messing up anything I'd already set.