The recommended way to install FuzzyFileNav is via Package Control. Package Control will install the correct branch on your system and keep it up to date.
Ensure Package Control is installed. Instructions are found here.
In Sublime Text, press ctrl + shift + p (Win, Linux) or cmd + shift + p (OSX) to bring up the quick panel. It will show a list of installable plugins.
FuzzyFileNav; when you see it, select it.
Restart to be sure everything is loaded proper.
This is not the recommended way to install FuzzyFileNav for the casual user as it requires the user to know which branch to install, know how to use git, and will not get automatically updated.
If you are forking for a pull request, this is the way to go, just replace the official repository with the link for your fork.
Quit Sublime Text.
Open a terminal:
cd /path/to/Sublime Text 3/Packages git clone https://github.com/facelessuser/FuzzyFileNav.git FuzzyFileNav
Restart Sublime Text.