Simply put, Futaba changed their minds on the programming after the manual was printed. The PCM-G3 channel order is like in the manual, otherwise, use how it sets itself up. You won't have any difficulties. ....Or you can just move the functions around to match the chart, if it makes you more comfortable. Just go into the Function section of the Linkage Menu to do that.

If you select the Wing Type of 2ail-2flap, most of the mixing is done for you. You can make some things easier. In the Function section of the Linkage Menu, set CAMBER to the desired control. Then, in the Model Menu, adjust the Camber Mix to make things move how you wish. If you use conditions, set the Camber Mix to Single in each condition, and you can have different settings for each condition.

Then, you can use the Aileron->Camber Flap mixer to make the flaps move with the ailerons.

Lots of ways to do this.

We don't know of any 12FG programming videos. Lots of FAQ's, though: http://www.futaba-rc.com/faq/faq-12fg.html