What you want, I assume, is as illustrated in 1, above. When the user types “ss” he gets the conjunct consonant instead of what we see in 2.
To do this we need to use Open Type features to create ligatures. If you search this site for VOLT, you will find a few threads on this free Microsoft software that can do this.
I believe that this is something on the todo list for Font Creator, but it is not currently available. See this thread to vote on Feature Requests