I'm assuming you don't use your terminal to start the browser... (in the terminal you probably can just type the browser's name)
If you mean the browser that will run whenever you click on a link/html file, then that depends on your Desktop Environment (GNOME/KDE) or window manager.
If you use gnome, you'd probably use
(search for browser, and change the path of "exec" to the new browser).
I think you can also just tell the browser to be the default, and it does the above automatically. Did you try that? Somewhere in the browser's tools, preferences, etc menu.
The flash plugin is in your home's directory's ".mozilla/plugins" directory.
You can download the plugin and change it as needed.