First, I would not use a Y on the flaps. Plug them into their own channels. Then you can follow the set up as shown in the link I sent you. Using a Y makes it very difficult to set things up correctly.

I also set my flaps up like this:

Set travel and subtrims to zero
Set switch to mid flap position (middle position on switch)
Make sure servo is centered and physically adjust the flaps linkages to get 50% flaps.
Then use end point on each channel to adjust zero and full flap positions.

You should look at Page 112 of the manual and consider using the flap trim menu as that may work as well if you prefer to stay with a Y