I am not familiar with bacteria additives but if by water conditioner you mean what I term dechlorinator then no: the air bubbles are emanating from your pump system.
As I have limited experience with my Eheim I did not post previously but you might try (which is what I did):
Place the pump in something which will hold water (I used a styrofoam box).
Get the pump primed and going.
Loosen the lid enough to let water start coming out and then reset the lid.
Repeat the process (as best I remember took me two times) until no air is observed in the return line to the tank.
The second time I installed the Eheim I could not get the above to work but it is way simpler than what I did the second time so hopefully it will work for you.