Hey scottr69, did you actually got it running?
How have you fixed the problem that you cannot choose the required exe File since it only lets you select folders?
I just put it in the folder next to shootergame folder (d:\YourAtlasServerFolder\) and when I right clicked on the grid to add server, the correct path was already there. You dont need to select the exe. Just the the folder that its located in, but for me it was already selected. I already had a 4 zone server running using batch files. I just put this in the proper location and added the ports I already had assigned and its up and running. Needs a RUN ALL button though, because they recommend starting them all at the same time (1 second apart for some reason).
Since I didn't have the issue you have, if you browse to the "D:\ATLAS\Shootergame\Binaries\Win64\" folder and select it. Does it not add the ShooterGameServer.exe to the end after you select the folder? Might be a bug that needs to be addressed as well ?