For stability, and paddling efficiency, your seat should be as low as you can use it. On the floor is ideal. This may not be a good position for other activities, say, fishing. May want an adjustable seat? A back rest and side braces (snugly bracketing your butt) will also add to both stability and efficiency.
If you have decking running along the sides of the boat, your knees can be tucked up under that. Padding will alleviate pain on knee caps. Then, position foot braces so that, when your feet and ankles are comfortable, your knees are firmly up against the underdecking. In this manner - back braced against the backrest, butt bracketed on the sides, feet firmly against the foot rests, and knees braced up under the decking - you are "wearing" the boat. Now, as your boat rolls and pitches, you keep your back upright. Your knees and feet control the boat. You can carve a tighter turn , say, to the left, by pushing on the right foot brace and raising your left knee. This tilts the boat to your right and it will carve a nicer turn to the left. Reverse all that for turning to the right.
If the above isn't possible, just put your foot rests where they feel right.
