In the portable firefox directory there is a portable firefox executible to start firefox. Also in there, I find a firefox directory and inside that folder is a firefoxe.exe executible. If I use the portable firefox executible to start fire fox and then later click on a internet link, the internet link uses the firefox executible instead of the portable firefox. Seems confusing having 2 different ways of starting the same program and then you have to duplicate the themes and extensions. I guess I am confused. Is there a solution to using just 1 of the executibles so I only have 1 set of themes and extensions?
Delete "firefox.exe" and firefox will not work. Delete "PortableFirefox.exe" and firefox will no longer be portable.
I hope hope that explains why both are important. You should be using PortableFirefox.exe (which uses firefox.exe).
Portable Firefox is little more than a front-end. When you run PortableFirefox.exe, it runs a copy of Firefox, passing some extra command-line switches and environment variables in order to make it portable.
firefox.exe exists because the copy of Firefox inside of the "firefox" directory is a stock version--it hasn't been modified at all. When you run firefox.exe directly, FF uses a profile stored locally on your hard drive. When you run PortableFirefox.exe, you get the expected behavior: the profile is redirected to the USB key.
To save yourself a lot of headaches, just run PortableFirefox.exe and ignore the rest of the directory tree.