Yes, but it's actually all in the MakeRwys documentation!
You can install MakeRwys wherever you want and then run it. It detects where your MSFS files are and creates the output files into the same folder. When you run the PF3 Update Database and are asked to select the Runways.CSV file you simply navigate to the folder where you installed and ran MakeRwys from. This differs from using MakeRwys with FS9, FSX or P3D as for those sims you had to run MakeRwys from the main FS folder.
Hope that helps