Proprietorship firm is not a legal entity, the proprietor is the legal person behind the firm.
So there are three ways a complaint can be maintained against such accused.
1. Against X the proprietor of proprietorship firm Y.
2. Simply against X, but some reference to the firm name must be given.
3. Against the proprietorship firm Y.
4. Against both X and Y (two accused)
Sr# 3 is lawfully incorrect, but the complainant can take refuge in the fact that he was not aware about the internal management of the firm and as per CPC (in absence of any other guidelines) the accused/respondent is required to state the facts about the firm constitution on first presence. Ideally Sr#1 is the best.. Incase of Sr#4, there are few instances of various HCs wherein the proceedings against proprietorship firm is quashed and continued against the proprietor only.