Only use one drive. The Amiga will spin them all simultaneously but it will read only one at a time.
You'll just slow down the process if you read more than one drive at a time.
As for the software, use Icycool's diskripper, which is just perfect for making images of a large amount of disks. You can edit the next disk's filename as you read the previous one and it autoincrements the number if you have a number at the end of the filename.
http://aminet.net/package/disk/misc/DiskRipper1.52
