Hej, you mean because of the bottom of your board (vee, concave, double concave etc) if you set in place the fin boxes flush with the bottom, then the cant will be wrong. Yes, so don't do that way.
Instead put the fin (preferably an old one) in its box, and when glueing it in place use a template (you make it out of anything, spare piece of plywood, cardboard, etc) perpendicular to the fin which holds it at the desired angle. You hold everything in place with tape while the batch of resin+crushed glassfiber cures. After that you can sand the protruding part of the box flush with the bottom of your board. I hope you understand what I mean, now re-reading myself I am not sure my explanation is super clear
