I have worked on a boat with auto pilot but never actually installed one but I can tell you this much
Auto pilot systems have a few different components.
The pilot computer system that comunicates with you Finder/GPS (this must also be compatible, most of the newer fish finders are check your finders menu to make sure. If it is nmea compatible you should also be fine)
A GPS and tiller senser for setting the course. the tiller sensor attaches to the Hydralic cylinder to let the system know where its steering
An additional Hydralic Pump that actually moves the motors independantly the Hydralic pump is driven from the boats battery and taps into the exsisting hydralic steering.
Now on on our cats two types of steering Cylinders are used single cylinder which has a rod straight through the cylinder with a motor attached both ends EG. Z-craft and double where each motor has a cylinder EG. Nova Cats and other big boats with serious horse power. as Rory said some cylinders are compatible and others not a quick google o your cylinder make and model should give you the good or the bad news
The big differance between the two systems is that you are in for a lot more plumbing with a two cylinder system as you will need to run double the pipes but thats not the end of the world
I hope I'm right about all this and not talking a load of K@K but I see nobody else had much to say so I thought I'd have a bash