Depends on the kit. Is it pre-drilled for a bridge? If not, I have found it easiest to do by putting the neck in position and letting the center of the dots guide me.
A better answer might be that, in retrospect, I don't usually calculate a centerline. If this is a p or j type build, the way I do it is by doing a dry-fit with the E and G strings installed (sometimes I use literal string). I put the pickups and pickguard in place. They I try to get everything to line up properly. Strings over the pickups. Strings about evenly close to the edges of the neck. Bridge 34" from the fretboard side of the nut to the g-string saddle all the way forward (toward the nut). If I can get all that to line up, I call it good. Eyeballing more than science ;-)
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