If possible you can feed them before nighttime and that would be fine. Turtles aren't that picky.. people say feed during afternoons because thats when their most active... I figure they'll eat it anytime.
As for feeding them in seperate containers, that's fine... what I do is I have 2 tanks, one's smaller and the big one they stay in. It's funny because the tanks are literally next to each other 
And I still have my filter and heater on the small tank so I just put them in there and feed them. I have a big and small RES too similar to yours, I figure they both eat till their full. (I make sure they both poop!) You won't be distracting them because they'll adapt to it. In fact after 10 feeding or so my turtles "beg for food" then when I prepare the stuff they float near the top and hardly move so I can easily pick them up and put them in there!
I don't think it's a problem feeding them at different times or different locations. It seems like it's your feeding them every day, I would suggest every other day as long as they get full during feedings. This will put less strain on u 