Some may think this is a silly question but I think the only silly question is an unasked question.
You can tell what the effectiveness of science abilities is by hovering over the ability icon in the tray. Once activated, does the effectiveness of an ability alter if you change you Auxilliary levels? For example, if you use Auxilliary to Batteries after starting a Gravity Well, does the strength of the Gravity Well drop?
However, there is one exception to this. Tractor beams and (possibly) tractor beam repulsors are affected by changes in auxiliary. Which is why a heavy graviton beam deactivates tractor beams when a ship gets hit by them (Aux offline mode for 5 seconds).