Hello Marlin,
Then the steps should be the following:
- print markers (we recommend to use 12-bit targets and use the pages from the middle of the document),
- stick them in the scene,
- take photos,
- add images to PhotoScan,
- use Detect Markers option form Tools menu,
- check that marker positions were estimated correctly,
- align photos,
- create Scale Bars for each pair of markers with the known distance between them,
- input corresponding distances in the Ground Control pane and check on such scale bars,
- press Update button,
- perform other processing steps.
Actually, you can detect markers even after the photo alignment procedure.