How can I interpret the "Count" output in the spreadsheet?
The count listed in each image is the number of objects detected in that single plane, irresepective of how they're going to be stitched later in TrackObjects
Is the highest number seen the total number of objects tracked in the group (or the total number of cells in the image file), or should I add all of the numbers in the group together to get the total number of cells in the image file?
This gets a bit complicated, and depends on the details of what your images look like (do you have a single layer of cells, or many layers on top of each other?). If it's a single layer, and you know for sure that the middle plane (or whatever plane has the highest number of identified cells) has every single cell represented, you could take the highest value of 'Count' across the planes and use that as the surrogate for your count for that image set. Alternately, if you go to the Object spreadsheet, you could look at the highest value of TrackObjects_Label for each image set- that will be the maximum number of objects found after stitching everything back together. If you have multiple layers of cells, that's likely to be the more reliable number.
My recommendation is to take a handful of images, count them manually, then compare both of those approaches to see if one or the other is consistently accurate for your purposes.