Eventually I hope to have an installer, but at this time, copy the pmra.pl (or pmra.exe if you're using Windows) to a directory in your path.  You'll need to put a PMRAcfg.txt file in:
Windows  - c:\documents and settings\your user name\Application Data
Linux - your home directory.

Edit the sample pmracfg.txt file appropriately. 

When you want to run Mozilla, execute pmra.  It will download your bookmarks.html file before Mozilla starts, execute Mozilla, and  then upload your bookmarks.html file after Mozilla exits.