If there is not enough overlap then you won't be able to align the two halves in photoscan.
It sounds like the background is causing you problems, and this can be masked out fairly effectively using the mask from model function under tools.
Align half of the photos where the background is consistent, then generate geometry, and then import mask from the model (Tools -> Imprt -> Masks - From model and active chunk only)
Then create another chunk with the other half of photos, and do the same.
Then your background should be more or less masked out in all photos, so you have the option to align chunks, or append the chunks into one and try aligning all photos together.
But as I said if you dont have enough overlap between the two halves then it won't work anyway.