I don't know if the SCD-1 is the same as the XA-777ES, but I have the service manual for the XA and it indicates the following:
Put a single-layer SACD in, close the drawer, and turn it off. When you turn it on again, it should do some basic realignment. This will work (according to the XA manual) for CDs, single-layer non-hybrid SACDs, and dual-layer non-hybrid SACDs. It will not work for hybrid SACDs.
To set the alignment completely (and to align for hybrids), you need to get the machine into test mode using a combination of buttons, and use the AMS knob to crank the built-in alignment system to do a complete job.
As I said, this is according to the XA-777ES service manual, so it's possible the SCD-1 also does something similar.