What I do is deflect the hinge all the way over (disconnect the servo, so you get extra movement).

Then fold the covering in half, length wise.

Now, stick the covering down inside the hinge gap, and seal one side with the iron. If necessary, shove the covering as far in to the gap as possible, then seal the covering to the other side.

When the surface is deflected, the covering is "bent", it doesn't try to smooth over the "V" between the aileron and wing (for example). But it keeps air from going through.

I wouldn't leave the covering flapping in the breeze. Fuel will find it's way in there, and evetually the covering flap will fall off.