On the illustration page, the lower area has two options: the Layout Placeholders tab and the Illustration tab. In the Layout Placeholders tab, each plot is represented by a test tube icon (Cytobank's symbol for an experiment file). Here you can drag labels and drop them in new places to change the order of the rows and columns. This can be useful if you have a large number of files; it's easier to manipulate the labels here than in the Illustrations tab.

Read a little more about Layout Placeholders here.