If you are using the .ADF files from the download directory here on the Amos Factory webpage, you need to run the AmosPro_System: drive with write-protect enabled. This will allow you to personalize your copy of AmosPro. It will not install if you do not do this. Once this is done you can use the installer application that comes with AmosPro to install to a hardfile. If you MUST access it from .ADFs directly, I'd recommend you use the automatic disk-swapper of WinUAE. (I'm assuming you're using WinUAE.)
If you are using a real Amiga the same rules apply but with real disks.
If you are trying to make a bootable disk with an application on it, I'd recommend you download all of the update disk images until you get to AmosPro version 2.0 which includes the compiler. The libraries needed by the compiled application will be the IEEE math libraries, diskfont.library, and possibly a few others from Libs:. You'll need the keymap from devs: I think, and system-configuration from wherever that is.
Can you tell us more about the configuration of your system or what you are trying to do?