Phil Wood ITA bottom bracket - chain line?


Dirt Disciple
Hopefully someone can help me out with this. I've mounted a brand new Phil Wood square taper BB with the ITA cartridge cups on a Colnago Master I'm restoring. Because of the way the BB and the cups are constructed, you are basically able to position the thing any way you want inside the shell, thereby changing the chain line.

This might be a stupid question, but I've never worked with this type of BB before and need some advice; what part of the frame should I use as "reference" when positioning the bottom bracket to achieve the correct chain line? I have now simply measured the distance between the ends of the square taper axle and the shell, but when I mounted the crank arms, they are of equal distance from the down tube, but not from the seat tube or the chain stays, where the difference is about 2,5-3 mm from side to side. Should I align the BB by using the shell and down tube, or by using the seat tube and chain stays?

Would really appreciate any help you could give me :)