APM 2.6 is the same APM 2.5 you know and love, but with one valuable change: this revision of the board has no onboard compass, which is designed for vehicles (especially multicopters and rovers) where the compass should be placed as far from power and motor sources as possible to avoid magnetic interference. (On fixed wing aircraft it’s often easier to mount APM far enough away from the motors and ESCs to avoid magnetic interference, so this is not as critical, but APM 2.6 gives more flexibility in that positioning and is a good choice for them, too). This is designed to be used with the new 3DR uBlox GPS with Compass, so that the GPS/Compass unit can be mounted further from noise sources than APM itself.
Note: APM 2.6 requires an external compass for full autonomy. If you are using APM 2.6 with a GPS module that does not have a compass sensor, you must use a stand-alone external compass. We recommend this one with this cable.
You can also use the new uBlox GPS with on board magnetometer (compass) with your existing APM 2.5, To modify your board, follow the directions here.