When you add an overlay to a project from the Image Tab, On-Screen Takeoff makes a copy of that overlay file and places it in an "Overlay" folder in the "Image Folder" as indicated on the Cover Sheet. Any alignment or resizing changes are made directly to that copy (the file itself is altered). If you add an overlay via the Cover Sheet, you bypass that copy creation process. Any alignment/resizing done to the overlay affects the base image on another Page because the changes are being made directly to the image file, not a copy. If you've used this file as the base image or overlay on another Page, you will be resizing/aligning it anywhere it is used which may cause takeoff to no longer match the plans.
We recommend adding overlays via the Image Tab, unless it is necessary to use the Cover Sheet method. If you use the Cover Sheet method, make a copy of every file you are going to use as an overlay, put it in an "Overlays" folder (where the original files are stored), and then use those copies as the overlays.