In order to get the full range out of your servo's, they must be installed in such a way that the entire servo range will map on the entire throw of the Flaps. If you want to use your control surfaces as pure flaps, with only travel down, you must have a 100% offset on the servos to get to the neutral (cruise) position of the flapss. This is the standard situation if you have one servo controlling both flaps, or you use a y-cable with parallel servos, or a tail mixer y-cable with mirrored servos. 

This is shown in the next image:



If you have a 'normal' servo install, with the control horns on the bottom side of the aileron, the situation is exactly the same. It may only be that you have to inverse the servo direction. That means that -100% will become 100% and vice versa.

We have used the term 'travel' to refer to the % of maximum throw that you want on a certain control surface, such as flaps or ailerons. They are always relative to the max throw. Flap travel of 100% corresponds to a servo position of -100%. Flap travel of 0% (no flaps) corresponds to a servo position of 100%.

If you have two seperate servos for the flaps, and have enough free channels, you could consider installing the servos so as to use the ailerons as flaperons.