Thanks guys. I've also heard that if I want to have the coil splitting options with my rotary switch I need to swap the magnet round or something?
Only if you want positions #2, 3 and 4 to be humcancelling. The normal magnet orientation is such that seen from the bridge the coils are south-north-north-south. Combining the inner or outer coils of both humbuckers would result in combinations of coils with the same magnetic direction which would only result in a humcancelling arrangement if one of the coils is electricaly out of phase with the other. That however would not give you the expected PRS sounds.
The solution is therefore to reverse the magnet in one of the pickups to achieve a south-north-south-north or north-south-north-south orientation (don't matter which way round). You will also have to change the electric phase of the pickup whose magnet is reversed (this is done with BKPs by soldering the black wire to the hot connection and the red wire to ground) - otherwise you get again out of phase sounds which are not humcancelling.
I did this myself with a Holydiver and a Crawler bridge pickup to work properly with the 5-way rotary switch (and voided the warranty on the Crawler but I am confident that I will never have BKP to take up on that anyway - the HD was bought used). If it's the first time you attempt a magnet reversion I would not start with a BKP - best to leave the job to a pro shop or BKP.
I'm thinking of swapping it out for a three way toggle switch, but want to consider my options.
That is IMHO the most practical option if your favorite playing positions are bridge humbucker alone and neck humbucker alone. These are farthest away from each other on the 5-way rotary.
Cheers Stephan