Sounds like your middle PUP might be a tad high for your particular picking style. You could tighten the screws on the middle pup lowering it in relation to the pickguard and putting some distance between it and your pick. This might tend to warm up the tone on that pup just a bit but you can play with it. You can also jack up your string height a tad but then this will change your fretting a bit.
Regarding where to pick - hey - I hope there is no secret rule book about this stuff, 'cause I am having a grand time making up my own as I go along. There IS a subtle or sometimes not so subtle difference in the out put depending on where you pick - find your own sweet spot for a particular configuration.
Have fun, hope I helped.
Bob
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