I recently asked my brother this question. This was his answer.
First, make sure the custom electric guitar is tuned the way you will normally be tuning it. (Folks who tune down for metal, for example, wind up putting less string tension on the neck than standard tuning).
Once tuned, adjust the truss rod until the neck is as close to flat as you can get it. That means no relief in the neck. You can check neck relief by putting a capo on the first fret and then holding dow the low E string at the fret at which the neck meets the body. Then look to see how much space there is between the bottom of the string and the top of the 7th or 8th fret. If there is a gap, we call that “relief” and it means your neck is curved slightly forward. Tighten the truss rod until that gap is gone or minimized.
Now that the neck is flat, adjust action up or down at the bridge. Once you have the action where you want it, you can try to address any fret buzz by tweaking the truss rod again, or going higher with the action…
Retune. Set intonation last by moving saddles forward or backward as needed until the fretted twelfth fret is the same pitch as the twelfth fret harmonic.