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I know I am probably feeding my turtle too much. But he's always searching the bottom on the tank for food, or when i sit near his tank he always come up to the side begging for food. I feed him 2 times a day, each time giving him 3 pellets. I believe he's still a baby though. He's only about 2 inches long. I had two baby RES, and one passed away because he came close to drowning, and ultimately got an infection and died. So now, my other turtle is growing, what seems like at a fast rate. He's started to shed too. How much should I be feeding him? And is it okay if i put feeder fish in his tank, or is he too small to eat those?

Turtles would eat pellets until they explode, so you can't trust them to let you know when they are full.
As long as you're feeding as man pellets as would fit into your turtle's head then you're not overfeeding him. You can divide that number of pellets into as many feedings as you like- some people prefer to feed throughout the day so that they can always toss in a pellet when their turtle begs.
If your turtle is growing too fast his shell will show it. The growth lines between the scutes will be very large.
It's normal that he's shedding, since young turtles grow so much in the first year, their shells have to shed in order to keep up.
As for the feeder fish, you can start feeding them whenever, just don't feed too many. They are a good once-a-month treat.