как means how, and что means what. So you don't say often, "How are you thinking?"; you say more often, "What are you thinking?".
как also means like, when used as a relative pronoun, and что also means that, when used as a relative pronoun.
My teacher often asks questions like us these: "Что вы думаете? Вы думаете, что Джей русский или американец?"
"What do you think? Do you think that Jay is Russian or American?"