Here is an alternative to the batch file launcher for Project64 1.6, if you can't get that to work for you.
Project64 Launcher by Scott Rice (aka "Meris" on Steam Communities).
This resolves the quotes issue and can handle situations where Project64.exe and the game roms are in different locations on your PC.
The direct download link (posted by "Meris" on Steam Communities) is
https://github.com/scottrice/Steam-Emulator-Launchers/raw/master/Windows/Project64/Project64-launcher.exe
See also
https://github.com/scottrice/Steam-Emulator-Launchers
and
http://steamcommunity.com/groups/IceRM/discussions/0/648814844716848346/
Put Project64-launcher.exe in the same folder as Project64.exe and set the Emulator Application Path to it.
If Project64.exe is in your C:\Program Files area, then before moving this file there you may need to Unblock it.
Otherwise it may ask permission to run every time you start a game.
The Emulator Parameters box needs no rom file tag and can be left empty.
You will most likely have set optional parameters (start in fullscreen etc.) within Project64 itself.
You can now add games via the Rom File (Emulation is enabled) browser box.
If you use Project64's ALT+F4 method to quit a game, then you will only exit Project64.
The launcher script will be only paused and you will see it's little icon in your tray.
Running a game again will open a new script.
With the launcher controlling Project64, you should use the Escape key to quit a game.
This closes the launcher which closes Project64.
NOTE:
If you're wary about using this EXE file you can always run Project64 as an application.