Okay, so I deleted the section and started again.
I used a section template which had 3 images horizontally on the page already. I changed the images to what I needed. (Let's call them images 1, 2 and 3). I added a code box underneath each image for a pop up text box (works).
I then added a separate image under each of these code boxes, images 4, 5 and 6 (with code boxes underneath), and repeated again for images 7, 8 and 9.
In edit mode, all looks great. In view mode, the images all line up along the left side of the page, in the order 1, 4, 7, 2, 5, 8, 3, 6, 9, decreasing