Markers - targets & points

[ruffy]

I am attempting to build a large object - a diesel motor which is 3.5Lx2Hx1.5W meters.
I used 10 cameras vertically every 18 degrees (200 images)
I placed around 30, 12 bit markers around the object.
I built each 10 camera section as a chunk (20 chunks).
Some chunks only recognise 2 targets which won't align or merge.
I have tried to create manual points within each chunk, however, when I merge, it does not sen to work.

Is there a correct procedure for adding points manually to chunks and then align thechunks with these points?