IME you don't. I tried fixing the gaps and it didn't work. I would say just worry about the bottom for catching leachate and the first bin. That's what I've ended up using. If you really want to make it flow through add another bin on top later on when the first is ready to harvest.

The best way to avoid fruit flies is proper feeding management. Freezing the food first is supposed to take care of fruit flies. It also helps since I have way too much to give them, I ended up w/ a hot compost pile also to deal w/ the rest. Make sure there is plenty of newspaper or bedding on top of food to prevent house flies. Keep moisture at a happy level also to prevent mites etc. Lots of indoor vermicomposters, the gaps really aren't going to matter.

I bought no-see-um netting ( the holes have to be that small ) and made a long tube out of it large enough to cover all my bins. I stitched a thin 1/8" bungee cord into the bottom end. And a draw sting at the top, so i don't have to take it off every time i feed.

You still have to do the freezing routine or eggs come in on the food and every time you open the bin they get out.