If the Base image and overlay is slightly out of alignment but the same SIZE, then use the Alignment Tool to nudge or rotate the overlay.
Right-click anywhere on the image and choose Overlay > Align Overlay Image - line with green circles at either end is displayed - this is the Alignment Tool.

 

 

 

Adjust the image until it is predominately grey (a purplish grey).  Once the images are aligned, deletions are shown in RED and additions in BLUE.  Adjust takeoff as needed to account for the changes in the overlay.

 

Adding Multiple Overlays to a Project