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Everytime I feed my RES with pellets in the tank it gets dirty couple weeks later. I got tired cleaning the tank every other week so I decided to feed my RES in a box container. Now it doesn't eat the pellets. I understand because it's not familiar eating in the container but I don't want to clean the tank everytime. Is it good to put my RES in the container everytime I feed it?

Is your filter up to the task? I stopped using a feeding tank since it didn't really make things easier for me.

You can try to start off with treats, things you know they'll go for. After a few days, try mixing pellets in and switching to that. Make sure you keep it consistent -- time of day, water temps, etc.

I feed my turtles daily in feeding containers, not boxes. I get some water from
the main tank and put them in the containers. Then I put the measured pellets
into each container. Lastly, I move my turtles.

The containers I use were from food containers, made of plastic.

It took a while for the turtles to get accustomed to the new feeding place. Just
keep trying.

Yes the filter is in the tank.

I guess it will be better if I get the water from the tank. I got the cold water straight from the sink and I don't think the RES likes it

In order to have the least jarring experience for your RES, use the water from the tank. I've heard using a bowl that isn't see through helps as well. I never had success with feeding outside the tank, but I didn't put in much effort. I felt it was more time consuming to take the turtle out everyday than to spot clean once a week.

What sort of mess are you having to clean up? Just poop? Or left over food? What size is your tank and what kind of filter are you using?

<<Everytime I feed my RES with pellets in the tank it gets dirty couple weeks later.>>
I don't get it.. What is the connection between pellets and the tank getting filthy two weeks later? Do you feed 'em once every 2 weeks?

Anyhow.. I think you should upgrade your filtration system.
With a large enough canister filter the water never gets murky/dirty, your only concern may be the nitrites going up in the long run, but that's it.