I suspect he is talking about the "built in" stock autopilots - prograde, normal, etc.
These AP's will ALWAYS reference the dominant gravity source, and this can't be changed. For most moon trips, this is a minor inconvenience. You should be close to aligned with the Moon before you make the transfer burn, and your first MCC's will be made while you are still in the Earth's SOI. If you need to make an adjustment while you are in the Sun's SOI ic can get a bit trickier. Teh Normal and Anti-normal AL's will still work OK since you should be close to aligned with the Moon, which is fairly close to the Ecliptic. The Prograde and Retrograde AP's won't be much use while in the Sun's SOI.
To make Prograde or Retrograde burns while you are in the Sun's SOI, open an OrbitMFD, and set the Ref to Earth, then press HUD. Now, the HUD is showing you your orbit relative to Earth, and you can manually point at the Prograde or Retrograde indicators.
For the lunar insertion burn, you will be inside the Moon's SOI by then so the Autopilots will be referenced to the Moon - which is exactly what you want.