Unfortunately I am not aware of any way to bypass the automatic scan. It’s best to ask this question again in the Slimdevices forum. The developers of the server can help you there directly.
You should find the two hard drives in the Squeezebox Server via the path /mnt/extdrive. All of your files should be in this folder. You can add media folders in the basic settings of the server.
The Samba Share is intended to make files on the hard drives available to other devices in the home network. If the Squeezebox server is running on the Pi to which both hard drives are connected, you don’t need to create a Samba share. If you still want to set up one, use /mnt/extdrive as as the path.