I'm very new to all of this however I made a slight modification to a
current extension by adding command line support to it. In order to
do so, I used the example XPCOM code (available in MDC under the
article titled, "Providing Command-Line Options"). Currently, I set
the paramaters included with the command line flag in the preferences
using nsIPrefService and, upon reading those parameters in the overlay
javascript, immediately reset that value. According to the "Working
with windows in chrome code" article, doing so is an acceptable
practice but I don't find it very clean so I was going to try to
implement some of the other data passing methods mentioned in that
article. I tried to use the FUEL application.storage object but it
seems it is not yet available from my XPCOM. Can someone point me in
the right direction?

Articles mention:
Providing Command-Line Options - https://developer.mozilla.org/en/Chrome/Command_Line
Working with windows in chrome code -