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I know that I should leave the lights for my turtles on for the same amount of time as the sun is up and i do on the weekdays. Is it alright if i turn the lights on on the weekends a little later and turn them off later? Or is that bad. Also, I turn them off when the sun goes down (around 5-6ish) but i go in and out of my room often til about 10 or 11. Is that bad for them?

For your first question, yes, it's fine.

For your second question, it's not the best, but it is also fine if you have no choice.

I have my turtle tank in my living room, and often I pull late-nighters, simply walking in and out, switching the living room lights on and off, or just sitting down to watch some TV in the early hours of the morning. They may or may not wake up, but they generally go straight back to sleep as soon as it's pitch black, and they sleep during the day too.

I could just cover them up with a towel or blanket or something. Would that work?

Yes.

I have my RES in the living room as well. When his lights are out but I want to stay up, I cover his stock tank with a big piece of cardboard. Since your tank is glass and light would come through the sides, a dark piece of cloth/towel would be good to use.