Only use an Emerald in the neck, where it's superb; the bridge Emerald is way too bright for this guitar. I speak from personal experience on this one as I've owned three PRS SE Custom 24 guitars and I still have one now.
The Holydiver works great in the bridge, especially if you like your mids. A smooth and tight(ish) tone with an even spread of mids. Strongly reminiscent of 80s Metal but with a slightly more modern flavour. Reasonably versatile for a contemporary pickup with good cleans and a superb lead tone. Using an Emerald in the neck is as close to perfection as you're likely to find. The AIV magnet gives it a bit of a vintage feel but the 43AWG wire gives it a lot more bite in the bottom end and it's far better at taking gain than a normal PAF - thick, creamy and fluid. Having a Holydiver in the neck is also an excellent option if you want your neck tone to be a little less thick and a bit brighter. Surprisingly, the Holydiver neck felt more vintage to me than the Emerald. A Cold Sweat neck would be a third option if you want something a bit more 'shreddy'.
A Crawler in the bridge will arguably give you one of the most versatile options you could imagine. It's thicker, darker and richer than the Holydiver, with a distinctive growl to it thanks to the 43AWG wire. It's quite a compressed pickup that has a lovely saturated feel to it. Cleans are excellent, it has the best splits of any humbucker I've ever tried and leads are incredible. It's not as tight as the Holydiver so won't take as much gain but I found that it could run from Blues to early Metal quite happily in standard tuning, Drop D, Eb standard and D standard. It certainly has a bigger operating window than the Holydiver with its natural home being Blues Rock and Classic Rock but more than happy to go either side of that. I REALLY loved this pickup in a PRS. The Emerald will also work here but I preferred using a Holydiver neck with this one because the brightness of the Holydiver neck gave me a nice contrast with the bridge and the more vintage feel of the Holydiver seemed to sit better with the Crawler. I wasn't keen on the Crawler neck but that's because with 42AWG wire, it's far more of a traditional PAF pickup and while the tone is very good, I always find the bottom end is too rounded and suffers under gain so I prefer my neck pickups wound with either 42.5AWG or 43AWG.
Although I've not tried it personally, I'd also suggest an Abraxas in the bridge. It's a bit like a Crawler taken down a step so not as thick, dark or compressed but still with a rich, smooth tone and would again be a very versatile option. Think of it as the ideal cross between a vintage PAF and the far more contemporary Crawler. As well as being a Crawler that's toned down a bit, it could also be described as a Mule on steroids, and often is. For me, I'd either use it with a Holydiver neck or a Black Dog neck because both are very similar being AV magnets and 42.5AWG wire.
