You do not have to save a file to a reference folder and refer to it in the container field. In FMP12 you set the container to use external storage and let FMS do the work. Read up on external container storage in FMS. You define the storage path relative to the Files location in the FMS Data folder. BTW, never ever move the container files or attempt to open them in a writable state. You will change them and that will make them unavailble to FMS, You will get the "File has been tampered with" message.
We probably can't help without knowing which OS and version you are using.
Thank you, I will look that up. I am using FM 12 Pro on a Windows 7 machine.