Stephanie,
I had flies too. I dont think they are problems. What has caused me problems before with row covers is aphids... They can multiply quickly when there are no other predators.
I've had to remove covers earlier than I wanted to in the past due to aphids.

What has helped me recently is that I've had many parasitic wasps that have made made many of my aphids into mummies.

see: http://www.cottoncrc.org.au/industry/Publications/Pests_and_Beneficials/Cotton_Insect_Pest_and_Beneficial_Guide/Beneficials_by_common_name/Parasitoids_of_Aphids_

Ok, so I have a late planting of cantaloupe and It is growing nicely. My Agribon just arrived today and I go out there to put it on and see several cucumber beetles having a wild party around my plants. So what about the cover? Do I just try to shoo as much as possible and then place it over? I mulch with straw and those dumb bugs crawl under that too. I, too, hate the idea of just trapping the bugs where they will have a lifelong supply of plant.

Did you make a choice yet? I probably would save the agribon for next year and battle the bugs in hand to claw combat.

However, a person more apt to use chemicals might try to use chems to get rid of the bugs then cover the plants.

I agree though that covering the plants with an active bug population is problematic to say the least. Maybe someone else has had to make that decision in the past.

Yes, by the time I read your reply, I had shooed away the bugs I saw, and placed my cover. Oh who knows. I even went out last night and attempted to hand pollinate the little flowers, I only found two females who's flowers were open, tomorrow morning, when the bees are more active I will remove the cover. I know they will do a better job than me! I don't use pesticides, for fear of harming the bees and other good bugs.I have also decided, before I do that, to cut down my cucumbers. I have an over abundance of them (I should have only planted 2) and that should make the beetles pack their bags and head elsewhere (yeah right). The cukes are so very randomly bitter, I dare not give them away because I can't tell if they will be good or bad. I am in the process of making 'cucumber mulch'! I won't miss them and next spring will plant less. Meanwhile, I'm crossing my fingers and hoping for a good patch of melons, acorn and butternut squash. In a couple of weeks, I will plant bush beans and take my chances on peas. It's so hot here now and I see no forecast of rain in the near future. I am such a novice at this, learning as I go. Any tips would be most welcome!!! I am patient and stubborn and will eventually get my soil good and healthy. I do need a plan though, to keep me focused and to avoid feeling frustrated and overwhelmed. I want to keep this fun, darn it!!!