I am just going thru this in my IV. I am playing thru a Marshall Class 5 and when I first got the amp I was unable to use the EQ - base had to be set to zero. In search of new pickups I found a lot of information on this topic at Seymour Duncan's Forum. There are several 335 players there who recommended lowering the front pick up on semi-hollows even with , or lower than the front ring. I have no experience with pickups but it piqued my curiosity so I followed their suggestions and am surprised and very happy with the results.
Since mud is not my thing I used the front pickup as my test piece.
First I set all the pole pieces level with the front pickup. Then I lowered the front pickup as described and immediately I could use the EQ on the amp. Then I adjusted the poles until they followed the contour of the fret board. I lowered the Low E pole (as suggested) a half turn below the pickup. This allowed me to use the Bass control on the amp. For some reason the Fender pickups seem to be sensitive to the B string on my guitar so I drove that pole down even with the top of the pickup. I would strum a 1st position G chord and listen for any strings sounding louder than the others.
I then set the height of the rear pickup to match the volume of the front pickup and followed a similar pattern for the poles. Some set this to be slightly louder so they can set the two guitar volumes the same, but have a little more presence on the bridge for lead work.
After playing this for several days I removed the strings and using a 6" rule and a line level, I leveled the guitar until the neck was level and then leveled the pickups front to back and side to side (pickups level to / parallel with strings). Then restrung and played some more tweaking the poles.
Finally, last night, I had the amp at volume fairly low. I turned the guitar volume to zero and then would pluck a string and bring the guitar volume up until I could just hear the string thru the amp. Then I moved to the next string and repeated. I would adjust the pole pieces until each string could be heard at the same volume setting on the guitar.
When it is said and done the poles look random and strange, but they are adjusted to each individual string voicing.
I had my guitar setup by a Luthier when I purchased it. He told me he get's it to play but it was up to me to dial it in. I thought "yea right" - well now I know - I will never pay to have pickups set on another electric, there are too many variables e.g. amp, string height, string gauge, pickup output, pick attack, etc. etc.
I took the guitar and amp to my last lesson. I told my teacher what I had done and wanted him to listen. I forgot all about it, but as I was leaving he made a very favorable comment on the tone - he was playing a 339 thru a Fender. (he can't help but eye IV)
There is some good info at Seymour's website by seemingly very knowledgeable people - check it out. It is rather enjoyable tweaking it around.
Edit - spelling, clarification