Dose per direction, anytime, day or night. Prolly wouldn't hurt to turn off the skimmer for 1/2 hour to an hour.
Will the bottom of the tank be ok while its small, I heard when the get bigger the get 100% dependent on lighting and may move it up then.
You want to put the clam where you want it. It doesn't like to be moved all around once it's in a spot it likes. Being small means it can't "produce" all it's food to keep it healthy. That doesn't mean it doesn't like light or to be feed food more than light. It just means it's growing fast and can't produce enough food. When it gets bigger it slows in growth rate and also produces more food, but at the same time doesn't need as much to keep itself healthy, thus is dependant more on light not food.
So, put the clam where you want it. It may or may not move, but the rocks on either side will help keep it there.
HTH