Hello FoodMan,
Are you using Standard or Professional Edition?
In Professional Edition there is an option to align chunks using markers. To do so you can place markers with the same labels in different chunks, and then they will be used for alignment instead of automatic process based on point matching.
We will be working on this option so that it is more clearly presented in the user interface.
With best regards,
Dmitry Semyonov
AgiSoft LLC