Set them where they sound good. The real trick is to make sure they are balanced. Just plug it in, and switch between them while playing a string (or all the strings) until they are balanced. If the pickup has adjustable pole pieces, I generally do this for both the E strings, and then adjust the rest of the pole pieces to match. If it does not have adjustable pole pieces, I do the E strings, and see how it works from there. It usually does a pretty good job, but sometimes some adjustment is necessary.
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