I use a screen lid, like for reptiles. Some people say that the screen will reduce the amount of UVB light that reaches the turtle, but in my opinion it can't be blocked much. Another option would be clamping the lights onto the box, but it makes me nervous having lights hanging over open water like that.
Another downside to my lid is a lot of water loss through evaporation, but I find it easy to stay on top of that.
The screen lid has a handy opening thingy for feeding and whatnot, and should fit perfectly if your box has about the same footprint as the tank
I find acrylic easier to work with than glass, easy to cut and you can drill through it (carefully).