Yes, mention it, and don't be shy about it either. Don't just say "I'm interested in Prof. Smart's work etc etc." Mention explicitly that you've been in correspondence with him for 6 months, have discussed your thesis topics etc., and (if it applies) he's offered to supervise your work contingent on you being admitted. Also, take him up on his offer to host a visit if you can.
Compatability with the department's research interests is a huge deal - and nothing looks better than a faculty member endorsing you. Don't be concerned about it sounding too specific. A PhD involves specific studies. Also, the admissions panel is going to be all faculty, so don't worry about sounding too technical/esoteric in describing your proposed work. They know their stuff.
Useless fun fact: Some departments at Stanford don't allow their MS student to go on the PhD unless they've already found an advisor who's willing to supervise their work.