Hi Lars,
The placement of markers on the pictures is more accurate, hence I wouldn't do this on the model.
In case you are processing geotagged images (i.e., acquired by a UAV/drone), run the photo alignment first and then import the marker locations (both have to use the same coordinate reference system). This should place the markers very close to their actual location. Manually move them to their real location (matching the GCPs) and you will see that the 'flag' turns green. Repeat for each marker on 4-5 pictures. You don't need to manually adjust a marker on all images. Use the FILTER PHOTOS BY MARKER option which accelerates this step. Then run optimization (magic wand icon in reference pane). Don't forget to adjust the accuracy settings before running the optimisation though.
Hope this is helpful.
Regards
SAV