Documentation topics are available from the documentation menu to the right. Some common issues and questions are answered here in FAQ and Troubleshooting.
If you have just installed FS-UAE, you might want to take a look at the getting started-guide first! As the getting started-guide mentions, you should ideally have Kickstart ROMs for the Amigas you want to emulate.
While you are running the emulator, you can open the FS-UAE menu or use keyboard shortcuts to control the emulator.
If you use FS-UAE Launcher, you don't have worry about configuration files, but when you use FS-UAE directly, you need to specify options either as program arguments or via configuration files.