I'm not sure what process you are doing to place the photos but there are several ways. I will highlight two.
1) You could file > place them (linked or embedded) in each on their own layers and size them to fit in each box.
2) Or you could drag them in from mini bridge and size them.
One thing I like to do, if they are all the same size is to create one box, using the vector shape tool, about the size I need it to be and clip the photos into each one. Now, I am not sure of your skill level in Photoshop so if anything I said sounds like gibberish to you, I'd be happy to provide a mini tutorial of what I am talking about.
Hope this helps.
96 is a lot of images to populate into a single Collage. My Photoshop Photo collage toolkit can only support up to 53 image because it relies on template to have alpha channels to map the collages images. Size location and shape. Photoshop has a limit of 53 Alpha channels. Template are simple to create ant the scripts can populate them with your images automatically, Interactively, Fully Automated and Batched.