You've bought the ball for a certain purpose, you're going to lay it out for a certain purpose, so, use the PAP that you would use when throwing that ball.
For example, if you want a ball for heavy oil and you want to play straighter. So, you buy a high-performance ball, drill it 3 3/8 x 3 3/8, and you would use the higher track's PAP coordinates to lay it out. Unfortunately, you may not find this useful if you want to use the same ball on different patterns, but it would be interesting to see what would happen if you lay a ball out with the high track's coordinates and throw it with a lower track.
OR you could ONLY throw with one type or rotation, therefore ONE track, and you wouldn't have to worry about such things.