For mechanical setting of the flaps, I dial in 1500 ms on the servo programmer, connect the flap servo to the programmer and then set the servo arm as close to centered as possible and the linkage so the flap surface is at or very near 1/2 flap. Then, when I connect the servo to the receiver, I know the flap is going to be centered at the middle position of a 3 position flap switch. Or if I use a 2 position switch, I am still O.K. with flaps full up or full down. Once connected to the receiver, I may use a little off-set in the transmitter to get the arm "perfectly" centered. Then I recheck the linkage to ensure the correct 1/2 flap setting. Every plane has a bit different recommended flap deflection settings. So one has to calculate and measure the 1/2 flap position when setting the arm and linkage.
If I get the linkage set so it is 1/2 flap at 1500 ms then I know I am good to go for full up and full down positions. If you set the linkage for half-flap with the Servo mistakenly at 900 or 2100 ms then you will not get full flap travel and it will be binding in one direction. I have seen where folks then limit the servo travel to avoid the binding. But they end up severely limiting their flap travel because they are only using 1/2 of the servo's travel. I use the servo programmer because I can see the setting (simulated Rxer Output).
I first get the arm centered when the servo is centered and then set the flap at 1/2 deflection. Then I just adjust the servo travel to get it up fully and down to the recommended full flap.
I have planes with Ys and planes w/o Ys on the flaps. For the flaps it is easy to just set the linkage and be done with it so a Y works O.K. for me. For Aile and Elev surfaces, then I go with the separate channels. If you got the channels use them. It makes life easier in the long run.