Backyard Drain Problem

I have a drain outside my garden floor door to the backyard. It connects to the sewerline underground – the pipe that enters the backwall to the house – that also is connected from the pipe that runs down the back wall from the roof (drains the roof).

The drain box has two holes – one that connects to a pipe with holes that I think runs parallel to the house (a French drain type of thing?) and the other to the sewer line.

The problem is that there is about 4″ of space below the holes to the bottom of the box, where water collects and sits.

Recently we’ve had an invasion of phorid flies which are know to come from sewer/drain pipes.

So my question is, is there a better box where the water wouldn’t sit at the bottom. I think my phorid fly problem is connected to the box, because they are not coming from my basement (dry – no sightings), and are definitely coming into the house from the garden back door and maybe windows. Also, I think the box breeds mosquitoes in the summer.