Hello Scott,
As cs suggested, to zoom into specific areas closely, it may be required to pan the model so that the area of interest is close to the center of rotation. Then it will not disappear during zooming.
There is also a different approach to marker placement. You can first create the marker instances using "Add Marker" command from the chunk context menu. After the marker instance is created, you may specify projections of the marker on the source photos. To do that, open the photo where the marker should be placed and switch to the marker editing mode using "Edit Markers" command from the Photo menu. While in the marker editing mode click with the right mouse button on the location where the marker projection should be placed, and select the marker instance from the "Place marker" submenu.
Using this approach it is possible to define markers without reconstructed geometry or model texture. The disadvantage compared to the model-based marker placement is that marker projections on each photo should be individually defined.
With best regards,
Dmitry Semyonov
AgiSoft LLC