Might depend on the pop-up template you choose, but for the 'Confirm' template you can align in to an edge or centered and change the size by pixel # or by dragging an edge (an the double line). Check out the right side of the screen under 'Position & Size' for alignment and pixel size.
If you are referring to the feature popup window on the map, it cannot be customized at this time, unfortunately. The style and all are inherited from Map Viewer/API:
I agree that this is needed. I have my pop-ups configured to pull into the Feature Info widget, but in the map, I would really like to adjust the formatting as it is rather awkward the way it is now, or alternative the option to have a second pop-up that is simpler.