Along with undercarriages, flaps can be quite a challenge to rig in an appropriate and reliable manner. A review of possible configurations might be a good way to start.
 

• Plain flaps - hinged in a similar way to ailerons. These are the simplest to set up. Hinges can be of the flat plastic with the metal pin variety, Robart Hinge Points, or plastic covering material on small powered models or gliders.

• Slotted flaps - more complicated, but can be more effective than plain flaps. The hinge line is below the wing so that as the flap goes back and down a slot opens up between it and the wing. Some of the airflow goes through the slot producing more lift than does the plain flap. Hinges can be made from two control horns with 8BA bolts as the hinge points (as shown below). Robart Hinge Points can be also be used as flap hinges.

The most common effect of flap operation commented on (complained about) is the pitch up usually experienced on deployment. Flaps are fitted to enhance low speed handling so throttling back and slowing down before lowering the flaps may reduce the pitch up. Radios with flap/elevator mixing almost completely eliminate this problem.

Flaps increase lift and therefore drag, making them useful for short, steep approaches. Airspeed needs to be watched to prevent overly high rates of descent leading to heavy landings.

Flap Linkages

The simplest flap mechanism is flaperons which requires an aileron servo in each wing mixed electronically to function as flaps as well. This setup is commonly seen in fun-fly machines, but any plane with strip ailerons can be set up this way.

The two cases below show the more conventional inboard flap/outboard aileron setup. Setups such as these allow flaps with broader chords. I have read that such flaps (25-30% of wing chord) produce smaller pitch-ups than narrower ones. Only experimentation would prove that. The
second example shows a single servo driving the flaps via a torque tube. Air loads on flap surfaces can be quite high requiring push rods to be straight and rigid. Ball joints can be used to minimise the "slop" that sometimes occurs with push rod end fittings.

These are but a few thoughts on the subject. Its an area where a great deal of experimentation can be carried out. Basic trainers lend themselves to this admirably and successful ideas can be used in scale models.

A book worth reading is, "Control Systems" by Jim Newman. It may still be available from Model Airplane News Pilots Mart.