There's a product by Zoo Med called Turtle Sulfa Dip. It comes in a blue box and isn't expensive. It's to treat mild shell infections. Why don't you get some and follow the instructions exactly and see how it goes. You might even try this first and see how it goes before trying the hibiclense.
And yes, following a hibiclense treatment you should keep the turtle in a dry place overnight. It won't hurt him. Just be sure that the place where he stays is very safe, dark and warm. When I've done this in the past I've used a large rubbermaid container with a lid (the lid has little holes by the handles for air) with towels in the bottom to make it comfortable.
