So I've got an se 245 I've swapped the pickups on and I've run into a bit of a roadblock.
This version has 2 volume and 2 tone controls as well as a three way switch. PRS has just a black ground going to the volume pot of each pickup with a white lead going to one of the tabs on the respective pot.

 I swapped the neck pickup for a humbucker sized p90 a while back and that went fine. Just 2 wires, no problem. Thing sounds awesome.
Well I've tried wiring the bridge pickup a dozen different ways and for lack of a better explanation its not what I've been expecting
I have a custom wound humbucker a guy made with the seymour duncan 4 conductor color code. So I tried wiring like a normal duncan with the green and bare soldered together to the ground of the volume pot and the black lead soldered to the tab of the same pot.  Like this I have no volume on my clean channel and barely any output on my lead channel.

So I tried it the PRS way with the black ground and white lead. My green, bare and red all taped off. This actually works out but the pickup is not what I'm looking for tonally; way too mid heavy. Wasn't chunky enough, I've already got a fat lead covered by the p90 so I wanted something that could do hard rock and metal. So Yesterday I bought a duncan custom bridge humbucker with a gold cover. I was looking for a nickel cover or preferably uncovered but it was from my local shop and it'll be an easy swap. But I digress. 

I wired it the PRS as that seemed to work best for the other duncan type humbucker. When I plugged in it sounded coil split, not a lot of output compared to my other humbuckers and very chimey. So I tried the seymour duncan wiring way and it sound similar but a different tone. Out of phase maybe? I dont really know the different between that and coil splitting. Either way, the red and white leads should be the only ones used for those wiring options, and no matter which way I tried It wasn't capable of the metal I've head it pulling off in a dozen videos. 

I've adjusted pickup heights accordingly as well, so am I doing something wrong? I've got a covered JB in the bridge of a another guitar that sounds nothing like this, so I'd like to think I'm making a mistake wiring it than having bad pickup taste lol Of course that'd be the cheaper option too  
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WildMiles96 From reading your post I am not sure if you have tried this but give it a shot.

Bare and Green to ground (back of volume pot) Tape off white and red (unused unless you are coil splitting usually) and Black wire to the switch.
pics of gear updated on profile 11/16/09