I have a Upside-down in my tank to, and I have a pretty similar story to thewatson27's. I had two, and one of mine died after a long time, but now I have one. I thought that this one had died too, after not seeing him for literally like 3 months, but one night I came home really late and flicked on the lights really quick and there he was! He likes to hide under my big piece of driftwood, and I never see him during the day, ever.
But I guess what I'm saying is, yes, they are a nocturnal species just like everyone says, and I'm sure they won't be as shy when they're in a group like it's recommended to do for them. As for the cover, I had almost the entire surface of my water covered with wisteria and pennywort, and he still would never come out, so idk if surface cover will coax him into being diurnal. You'll just have to live knowing that you have fish that's up when you're sleeping! =/