Unfortunately, with pickups it's imperative to experiment to really know what's best with each individual guitar. IF you want it to sound it's best. Which, admittedly is a PIA. For example, the USA Charvel SoCals from 08/09 came with DiMarzio Tone Zone in the bridge...I can't stand that pup. Just not for me...I have 4 sitting in my 'miscellaneous junk' box. But, I had an 08 Candy Tangerine SoCal that had GREAT tone....as good as anything I've owned/picked up and it had the stock TZ in. I ended up selling it because I found an 84 Charvel for 799...listed as a model 1 Lol....but before I sold it I swapped the TZ for a Duncan Custom...the TZ sounded better in THAT guitar. First time that ever happened. I always swap in/out a few pickups that I have here just to see if one fits better than the rest. Time consuming yes, but worth it in the end. I have an MCP Angel Dust, Duncan Custom and RTM, 1983 JBJ, and Wagner Iron Man for my experiments here.
I would also add, with a JB and any pickup you really have to experiment with the height to get different responses/tonal changes. But you guys probably know this already.