If you are running OS X, I recommend putting your MultiMarkdown folder in your Library Folder, specifically:
~/Library/Application Support/MultiMarkdown
This will allow other programs to share one installation of the MultiMarkdown code, and make it easier for you to keep things up to date.
In the future, I hope to release some installers to make this process easier, but Apple’s Installer tool is woefully unsuited to the task…
Fletcher T. Penney
http://fletcherpenney.net/MultiMarkdown