To begin, we'll take a hint from the LOC tutorial and select reference points near the corners of the image. Angles are best, because they define a point at their apex. Right angles are even better, because it's easier to line guides up at right angles.
The points should be as close to the far corners as possible because that's where the distortion will be worst. Unfortunately the exact corners generally don't have a visible reference point, so we just get as close to them as we can. The references, obviously, need to be at places that are visible on all three channels.

Why use the Green channel as the target?
We know that Prokudin-Gorskii used a single-lens camera, we've seen it. We know that he thought of "RGB" in much the same way we do today, by the way he ordered the colors, putting green second (or in the center). Logically, he would have lined the center of the plate behind his lens for a direct shot, and fired the other two colors to the opposite ends of the plate.
Therefore since the center image of each plate is the green channel, that channel likely was the straight-on image. That would make it the truest representation of the subject (and might also hint at why it is generally also the largest). The ones top and bottom would therefore have been done (I assume) with mirrors, and are screwed up. So we'll adjust those two, using the green channel as our target.