As with all menu items in the afni GUI that let you choose from a list, you can use this trick; right-click to the left of the button, and the list shows up in a scrollable menu instead of a large fixed size list. This works with the atlas region selection too. You can also use the Show Atlas Colors to color regions, but it doesn't let you modify the regions there. You can choose the atlas that works with by setting AFNI_ATLAS_COLORS to that atlas.