Hello sambagis,
To create the markers that are to be used as valid tie points you need to:
- open the image in Photo view mode by double-clicking on its label in any pane,
- locate the position of "manual tie point", right-click in the location and choose Place Marker -> New Marker option from the context menu,
- open another image where the same point should be marked, right-click in the proper location and choose Place Marker -> <marker label> option from the context menu,
- repeat the previous step for all the images where the manual tie points should be present,
- repeat the same steps for all the manual tie points,
- select all NA (not aligned) cameras in the Workspace pane, right-click on selection and run Align Selected Cameras operation from the context menu (the initial matching via Align Photos command should be already completed and alignment for incorrectly aligned cameras should be reset in advance).