Thanks for the photo - it helps my explanation. It just happens I’m wrestling with the installation of these on my 2005 FZ6 also.
The 2 empty holes next to the mirror stalk (on both sides) are supposed to hold small rubber bushings that are molded around a threaded brass fitting at the lower/inserted end. Each bushing gets pushed into a hole and then accepts a short screw fastening the wind screen to the fairing.
These rubber mountings isolate bike vibration from the screen.
In total there are 4 rubber bushings and their screws, and a single screw (no bushing) at the lower, front point of the screen that completes the attachment to the bike.
I need to replace my set because the bushings have deteriorated, so post any source and part number.