Which model do you have...the P-Rails (neck) or the P-Rails+ (bridge)?
I've found that the P-Rails+ is just way too strong and looses clarity, especially in series. But the neck model works great in the bridge. I mount it with the Rail coil next to the bridge and an A8 magnet next to the rail to compensate for the loss in output and to beef it up (tonewise) as well. To help reduce the potential muddiness, you can put an A4 next to the P-90 coil. This helps a lot, but the P-Rails will always sound very heavy in series mode.
I find that in all of my guitars that have P-Rails in them (3 or 4), I use the P-90 tone at least 85-90% of the time. I use the parallel tone about 10% and the rail tone about 5% of the time.