I need to add some more instructions to the MultiMarkdown Readme now, as it is a bit more complicated if you want to use the math features and the XSLT transforms.
More details to come but:
To use the math features requires piping the raw MultiMarkdown text through the php tool first, and then the result is passed to MultiMarkdown (or regular Markdown for that matter - the math processing is already done).
Because of issues with namespaces and the MathML code, there is now a postprocessing command
Included in the MultiMarkdown zipfile are some example command line programs that demonstrate how to string everything together. I highly recommend setting up a work flow that works for you, and then using an automated tool to handle it for you. In that regard, I think the MultiMarkdownTextMateBundle is a great tool.