The PRS Core guitars ship with .010s, the SEs ship with .009s, except where you would expect otherwise, like the baritone (.014s - duh) or the HBs with piezo (which have .011s).
The typical core/S2 CU22/CU24 set-up seems to be just fine for shifting between .009s and .010s and .011s, and I would guess the SEs can go from .009s to .010s just as easily. Anything thicker might need a slight nut filing or intonation adjustment or maybe truss rod tweak.
If your strings are going out of tune, I would first check whether you keep the guitar in a steady environment (do you open/close nearby windows a lot?), whether your hands are causing the strings to corrode early, or maybe just stop using EB strings? They are cheap, but I am under the impression they aren't as good as the D'Addarios that typically ship with PRSi.
Dunno - I can pick up any of my PRSi after not playing it for days/weeks, and usually at most one string (the G-string usually, for some reason) will need a slight tune. Most times nothing really needed. Or maybe I'm just tolerant of slightly out-of-tune guitars...