The best way is to work it out with your supplier. They probably know how.
Second best way is to find something similar and copy it. That’s why I like the project boxes so much. They’ve been around for decades, so they are engineered to just work.
Third way is to wing and build in too much tolerance so that you can always reduce the tolerances later by machining in the mold. Basically, make everything fit a little loose and then adjust.