FileBot

In the FileBot folder there are two files:
filebot.exe
filebot.launcher.exe

They're both the same size so which one should I use? There is nothing about it in the 'manual'.

FileBot will create a shortcut named FileBot on your Desktop and in your Start Menu. That's the one you will want to click to start FileBot.

That shortcut will indeed link to the filebot.launcher.exe executable. An advanced user might call filebot on the command-line, and in this case CMD or PowerShell will run the filebot.exe executable. Either way, users do not generally navigate to the Program Files folder to launch programs, that's technical details you don't need to worry about, that might change over time, that are different on each platform.