If I open up the mod I'm working on as the active file...and X in two plugins (Lets say Tamriel Npcs Remodeled for example) but they arent active, when I save my mod, will it add my changes to those X'd in plugins too? Or will it add the changes from the X'd in plugins to my mod? Or will neither happen and only my mod gets saved?

Changes get saved to the active mod only. If mymod.esp is active and something from anothermod.esp is edited then that edited item is added to mymod.esp.

You cannot use resources from another ESP. You can only copy them as wetblanket noted above into your own active plugin.