How to reset the orientation of the navball?

[Dr Gorilla]

Basically, I attached two modded Aeris 4 SPH ships to my rocket and landed it on the mun, but when I try to fly the Aeris 4 the navball is rotated 90 degrees. As a result, A and D move the ship up and down, while W and S move the ship left and right. Is there any way to fix this?

[Gargamel]

It's difficult to say, as we can't see your whole ship in the pic.    This 'error' is usually caused by the main control core/cockpit not be in control of the vessel.  Right click the cockpit or the probe core, and select control from here.   If your main control core/cockpit is rotated, the Navball will line up with the core/cockpit like you see here.  Keep changing your cores until you find a good one.   

If not, you might have to learn to fly sideways, or flip your monitor on it's side.    

[Snark]

14 hours ago, Dr Gorilla said:

when I try to fly the Aeris 4 the navball is rotated 90 degrees.

By any chance do you happen to have a probe core on the ship?  And is the probe core rotated at a 90 degree angle about its axis?

The orientation of the navball reflects the orientation of your "control from here" part.  If it looks screwy, it's most likely because the part was oriented "wrong" when you built the rocket.  (This is an especially easy mistake to make with probe cores, since they look fairly radially symmetric and it's not super obvious when you're eyeballing them which way is the "up" direction.)

If you have some other part on the ship which is clearly visible as being right-way-up (such as, for example, a cockpit), then clicking "control from here" on that part, as Gargamel suggests, could help orient the navball to that part's POV.