Are those curly winged or vestigial winged fruit flies? The completely wingless fruit flies are much easier to contain. I used to have true wingless flies, it was like dealing with ants. Just shake them down and tap them into a cup to feed from. Unfortunately I allowed them to die out. I recently picked up a colony of the curly winged flies and they're a MUCH bigger pain to deal with. They only fly a couple of inches but it's enough, they do this hop/fly thing that lets them spread out pretty quick. The true wingless flies will hop a little bit but it's not as much of a problem.