Hi, both sentences are grammatically correct but they are different in terms of `construction` which in my opinion (I`m a Pole - I may be wrong) implies a little bit different meaning to those examples (at least in my language).
The first difference emerges from how the sentences are built and you should take allowance for that if you are not aware of it:
"I think you do not understand" - the pattern here is: a)I THINK + b)anything else that is a ... stream of your thoughts
"I do not think you understand" - the pattern here is a)I DON`T THINK + b)anything else but determined by the a) part
Or maybe what I`m writing doesn`t make any sense because it depends on the culture you come from. For example: when I`m looking down on somebody I would say "I don`t think you understand it" - I would use it when being malicious to somebody, saying " I think you don`t understamd it" would be normal, let`s say that "I think..." is 100% of what you want to say and "I don`t think..." may be 105% if you use it that way.