This isn't a long term remedy, but I know a little trick to get rid of ALOT of them...
Get some Apple Cider Vinegar (has to be Apple Cider vinegar or it won't work). Put about 1/3 in a ceramic cup (i.e. coffee cup), cover the top with Plastic wrap and poke several tiny holes. The fruit flies are attracted to the smell of the apple cider vinegar and get trapped inside the cup and either just die or drown trying to get to it.
I would use as many cups as necessary throughout your house and wherever you are having the problems. Empty and clean the cups once you see a large amount of dead flies inside.
Also, make sure you are keeping dishes clean and put away any fresh fruits or vegetables as they are attracted to the smell of rotting food.