I have a Seymour Duncan JB bridge pup in my PRS CE custom, and am curious as to how close or far to the strings it should be to maximize its potential.

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I'd email Duncan and ask if you want a definite answer for that pup only. A general rule is you get a more mellow bass/midrange tone farther away and a hotter more trebbly/high-mid tone with it closer. I'd start with about 2mm clearance (strings to polepieces) and see how you like the sound, it's easy to move it around and you can dial in the tone you want pretty quickly. Also try having one side heigher or lower than the other to accentuate either the bass or treble strings if you feel one is lacking.