As far as I am aware the Poly Scuplting Tool will always see them as seperate geometry. Therefore you wont be able to get rid of the problem unless you combine them together and merge the vertices, thus creating a new peice of geometry. This is not what you want to do so you are pretty stuck.

Can you put in a screenshot of whats going on and give some info on what ur trying to acheive so other may have a suggestion or tip on working round this issue.