I have a plane with two aileron and two flap servos (Aero type RA,LA,RF,LF) and I'm trying to set it up to have two levels of flaps. Currently the switch just operates the servos to the end point set on Right Flap and Left Flap.

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Frankly, your description of what the problem is versus what you want to do is not clear.

Assuming you're in the Aero side of the radio and you didn't change much, it comes set up with a VR assigned to flaps plus switches 13, 14, & 15 assigned to flaps as well, with end points using only half the channel.  Note Sw 13 isn't actually assigned to anything.  The Flap channels just go to the position set by the "N" entry in the Surface menu when nothing is active (or to the VR commanded positon when it's active).

If you only want switches, you need to go to the VR menu and INH the assigned VR.  One of the first things I do when setting up a new model.

Then I go in and reassign the Flap Epa's to use the entire channel -  N = 100%, 1 = 0%, 2 = 100%.

From there, I do the mechanical setup of servo arms and linkages to get Sw 13 ( N) = Flaps up and Sw 14 (Pos 1) & Sw 15 (Pos 2) somewhere close to the deflections I want.  Followed by tuning with the EPA's.  Note you may have to Rev one or both channels.

So what are you trying to do?