Bear in mind that flaps on a short final might lead to a tip stall especially if you happen to be flying a warbird.
Don't get tip stalling confused with an uncoordinated stall which results in a wing dropping. Tip stalls happen in swept wing aircraft were the onset of the wing stalling starts at the tip. A standard model does not tip stall.
Also keep in mind that the flaps aren't the reason for the aircraft to stall. Flaps increase the angle of attack on the inner portion of the wing. When you stall with flaps out, the root of the wing still stalls first. That being said what people do that cause the model to stall is fail to lower the nose when the flaps are extended. Since you are increasing the AOA on the wing you reduce the body angle. If you keep the body angle the same with flaps as you did without flaps you run the risk of stalling the airplane.
The best thing to do is get the aircraft in the landing configuration and take it up and do multiple stalls and a lot of slow flight so you can get used to the stalling pitch attitude.