I agree with the advice given.
The ‘beep’ ‘beep’ noise was probably a mild distress call, ‘It’s going dark and I’m not in the right place!’ Don’t feel bad about it, they’ll soon learn the routine. Just cover the top, back and sides of the cage and a little of the front at first; they’ll very soon begin to realise what’s happening and ‘go up to bed’. Then you can pull the front down further, but still leave it up a just little off the bottom.
The food dish perches are fine; as Kellie said, they maybe don’t recognise how they can use it, or maybe it’s just a new material sensation that they aren’t yet familiar with.
The link that Jesska posted is good, it also suggests how to clean the wood.
It’s good that you’ve made the long dowel the lowest perch, as you’ll probably find that they use it the least - For that reason, I wouldn’t panic and disturb them by replacing it immediately, give them a couple of weeks to settle down for now.
If you like a bit of DIY, a member in the past has also carved and then carefully sanded a dowel perch to create a more varied surface:
I notice that you have fixed the slide up food doors with what appears to be twist ties. These tend to contain a metal strip that is toxic to birds. I suggest that you remove these and try to use some wooden or plastic pegs instead. Alternatively, you could fix permanently with zip ties and used different bowls.
Best of luck, I’m sure they’ll be settling in soon