If you selected Adjust alignment in design module in the check alignment wizard of the scan module, the Scan alignment page will pop up as the first page in the design wizard.
Rotate both scan objects to have a similar rotation. Then, click a common point on the die scan (on the upper 3D viewer) and the jaw scan (on the lower 3D viewer).
Check the result of the alignment. You should see a green surface on the important area of the aligned part. To correct the alignment, click another point to restart matching, or change the rotation and click Restart matching.
If the alignment is fine, click Next.