I'm looking for some advice on how to get my amp/petal settings right. Currently I am using a low end amp which may be most of the problem. Hopefully I'll be getting a B52 next month. Anyway, no matter how I have it set up, the low E string (6th) seems to drown every other string out. My amp only has a level, low, mid, high, and reverb knob. I'm also using a Boss ML2 pedal with level, low, high, distortion knobs. I'm just looking for some suggestions on how to set these knobs correctly. I'm currently playing a lot of Opeth if that's of any help.
you might have to lower the pickups on the thicker side of the strings.
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If you take a look at your pickups you'll see a screw at the top and bottom of each one, generally tightning these raises that end and loostening lowers it. It sounds as though they might be a bit uneven already so if the pickup in question is noticeably higher on the low end bring it down till it's even, if it's already pretty even maybe just lower it a bit still but don't get carred away. Do it with your guitar plugged in and make small adjustments, play fr a bit and see if there's any difference and then adjust a little more till you're happy. Also, if you've got your bass boosted really high on your amp/pedal it might be causing that string to boom the way you describe, maybe try just cutting back on it a little.
Hope this helps