Do you use ‘How do you mean?’  If you do, in what situation is it used?

The intention of your statement is unclear, so please explain it in more detail, specifically telling us how it is different from the other possible similar meanings.

It is a way of asking for more specifics when the idea of the statement was overly broad and thus different answers might apply, depending upon the specific use that was intended.

Boy this soup sucks.

How do you mean? Too salty, too bland, too watery, not enough meat, too much tomato, or what?  Cannot fix it if I don't know how it sucks.

You say "What do you mean?" However if someone says something ambiguous you might say "How do you mean that?"

"I've never met anyone with a mind like yours." "How do you mean that?"

I have said this, but not very often as it is kind of slang-y. It basically is a question you would ask someone when you don't understand what they are trying to tell you.

Example:Dave: You have to prime the walls before you can start painting them.

John: How do you mean?

** John doesn't understand and needs clarification.

If someone said something unclear, I'd say, "How do you mean that?"