Most folks will mount the neck, put a low e & a high e on, align the neck for equal reveal on outer sides of both e strings so that the neck is well centered, then complete the mount by tightening the neck mounting screws.
Then, what most folks do is then lay the loaded pickguard on the body, with the same string setup, and align the pole pieces appropriately under the strings, tape off the pickguard, then commence with the pre-drilling of the holes, and mounting.