Welcome to the forum.
I would like to clarify whether your guitar is a PRS SE Custom with 24 frets or an SE Singlecut 245? Which bridge does it have, fixed or vibrato?
So, turn the pedal levels back up to where they were set for your Stratocaster. Ride the PRS volume control to govern the intensity of overdrive saturation.
Yeah if you have room to play with your tone knob I think you'll like any of those. Pearly gates is one set I wanted to try, warren and dickey know what's up
Just make good use of your tone knob if the treble is an issue. Yes. You wire directly to the switch for an SE. Join the two wires (I forget the colors on duncans) but then ground goes to the obvious solder pile on the switch that is ground, and the hot lead goes on the switch. You'll see the ground and lead if you look at the switch, but they are 2 conductor. The other 2 should be braided, soldered and covered with heat shrink or electrical tape if that makes sense
do the PG's work with the 3 way switch on the SE?