Okay, as an "inventor" for a private firm, you probably signed an agreement stating that all of your work done at said company is owned by the company. I think, therefore, that it is out of your hands--if the company wants to file a patent, they can do so.
Notice how Microsoft patents, for example, are owned by Microsoft Corporation, not by the individual coders who came up with whatever algorithm/mechanism/whatever the company is trying to patent.
Therefore, I *think* that your boss is just requesting your help filing and managing whatever the software does (assuming he is not a techie and can't write out the algorithm/flow charts himself). If you refuse to help him, he could still get a patent, and probably fire you, too...
HOWEVER! I am not a lawyer, and this sounds like something that should be verified by one. I would recommend talking to a patent attorney as well.
Hope that helps!
