"Auto Pilot" And Existing Ships

So, I decided that I'd set up one of my ships to do patrol, which I had done a complete overhaul of by grinding apart the old one, and re-attaching everything to the cockpit section, after having widened/lengthened the entire thing, and added a lot more to it.

Only, there is one problem.. It treats the top of the ship, as the front, and the back as the top of the ship.
Example of what I mean:


Any clue how to fix this? IF its fixable?

 

Yeah, reorient your remote control. Remember, the triangle on the side of the remote is on the bottom of the remote, and is pointing to the front of the remote.

 

Oooooh, okay! Didn't know that. First time actually using a control block. Thanks!