If done right, one side is all you really need for just about any size model aircraft. That's all I do, and I have planes as large as 96" wingspan that never had problems. There isn't any great forces on the hinge gaps to warrant doing it on the other side too. The clear Ultracote (my preference) should last as long as the rest of the covering on the plane.

One trick I've learned to do is to fold a crease down the center of the strip of Ultracote to form a "V". This helps me to center the strip on the hinge gap and allows me to iron down one side of the "V" without getting the other side stuck down to the wrong position. I just eyeball it and fold by hand, but you can use a long straight edge if you prefer. The "V" does not need to be exactly symmetrical. Just make sure you cut it to stay inside the TE and LE of the control surfaces.