PN makes changes almost exclusively through either feature modifications, which are things like the visor overlays, sprint, and stealth changes, and through gameplay modifications, which are pretty much exclusively confined to the Rebalance module. Rebalance works by altering the game settings, which are used by the game engine to derive pretty much all statistics, such as how fast you get hungry, and how far away NPCs can detect you in various circumstances.
So to answer you question yes, the PN sneak difficulty will carry over just fine. In fact, so far as I can tell, and with the exclusion of the Equipment module, pretty much every PN change carries over fine, just maybe not with full integration in the case of FO3 specific items (like outcast armor and DLC stuff).
I would not suggest running with FWE and PN at the same time, nor would I actually suggest using FWE at all. It was great for FO3, but we have so much better now, and the changes FWE makes are so core to the game that it would be a nightmare to test everything.