I have gone through this process a few times. The SCSI2SD will indeed work very well with workbench 1.3, but it's a bit of a cumbersome process the first time.
This is something I've been meaning to make as a "How To" article for some time. I am at work at the moment, so I do hope to offer more detail later, but from a high-level:
I use
HDInstTool instead. (I have mine set to English. IIRC it was set to German and I had to change it, and saved it this way.) With HDInstTool it will see your drive, and you can partition and format it as you wish.
By the way, what size SD card are you using? I've found smaller cards are much more responsive and take far less time to boot in non-accelerated Amigas, which is very nice.
I assume the SCIS2SD will be your only drive in the machine. Be sure to check the "bootable" option, too.
Are you re-using the scsi.amhd driver?
HDInstTool has been the ticket for me.