Confusion happens a lot with dogs, especially if they are younger. Clickers do work great yes, and so does positive reinforcement.
Akasha had this problem after we taught her the command "Lay down" - I'm not really sure why this is confusing for her to determine "Sit" or "Lay", but something you can try is we use the method of voice change.
We try telling Akasha to "Sit" in one voice - then "Lay down" is in another voice. I know this sounds weird but it has helped her realize what we are asking.