I use regular sewing thread, mostly polyester. Some prefer to use all cotton. I do use the same thread on the bottom as the top. I don't believe bobbin thread would work very well. The color would depend upon whether you want it to blend in or be contrasting to show up a design.

I have used regular thread and embroidery thread. I would use the same in the top and bottom - bobbin thread is not as strong as regular thread.