Any tips on this?
I have the Seymour Duncan® Hyperion™ Passive Humbucker Pickups.
Generally speaking the closer it is to the strings, the more bass it will pick up. Other than that, I raise them as high as I can without bumping into the strings when palm muting, start lowering in small increments and stop when I like what I hear. In some cases too close might cause warbling, sustain and intonation issues b/c some pups have extremely strong magnets and exert such a pull on the strings that it causes the above mentioned troubles. I’ve seen this phenomenon at work with a set of Black Winters. On the other hand actives, like EMGs, can go as close to the strings as they can, because the heavy lifting is done by the preamp, not the magnets.
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Great answer @nexion218 ! The middle pick up in my Ibanez has to be pretty low although I play in between the bridge and middle.
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Thanks @kiko! 
Is it low because it gets in the way physically or because of having to match it’s output to the split coils of the humbuckers in positions 2&4?
By the way your comment about the middle pickup made me realize that I overlooked on aspect of the pickup height setup in my initial answer. While it is true that the lower the pickup goes the less “bassy”, but it also loses some of the overall power/volume. Another thing that affects power/volume is the position of the pickup in the guitar: the closer it is to the neck, the bigger signal it will produce due to the wider vibrations of the strings. Close to the bridge the string movement is barely visible, thus the thinner and more focused sound of the bridge pickup. Above the neck pickup we can clearly see the string vibrating, producing a fuller and louder sound. So in order to have a balanced output from a pair of pickups one has to keep in mind that the neck pickup will produce a way stronger signal due to it’s position, so it will usually be sitting lower below the strings than the bridge pickup. This could be somewhat altered if one is using a matched set of pups where the neck pickup has a lower output and wound to account for the different signal it has to pick up than the bridge 'bucker, but still, it will be lower.
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