Look thru the unzipped folders to find one you would like to try.
Copy the "fakehdr.fx" file into "C:\Program Files\Project64 1.6"
Now run Project64, and go to options > settings
In the Video (graphics) plugin, select "Mudlord's Rice Video Build 6.1.3 - DX9. NOT 6.1.4! Then push OK to close this menu.
Start the game and it should be working! You can obviously try out different shaders, but you will need to copy them into the "C:\Program Files\Project64 1.6" directory and restart the game each time you do.
NOTE: Whenever you start a game now, it will look for a fakehdr.fx file. If you don't want to use shaders, simply go to settings and have it use a different video plugin.