From what you are saying you have Fungal Gnats very bad. Gnatrol is what you need you can put it in your res.

If you are using CO² you can turn it up above 3k ppm for a few hours it will kill the ones out of the water.

They eat roots but are more of a pain in the ass. You need to install an inline filter in your res too. That keeps them from spredding through your pump system too.