Mikee, I was able to figure this out and I received confirmation from John at SquareConnect after I did as well. Basically, you have to create a new 'theme' under the themes tab and save it under whatever name you like. Then you can drag and drop PNG files onto any of the specific buttons that you want to use. I actually chose buttons I would never use and replaced those buttons with the logos I wanted to use. You must make sure to save the theme after you add the icons.
Also, like Legend said, you must remember what buttons you dragged your icons too. When you go to drag the button with an icon on it, the icon does not show up in the list. It is still an image of the original button. When you drag that button over to the layout, you then need to make sure you select your saved theme from the dropdown box towards top left. Right under the dropdown for 'iphone' or 'ipad' layout.
After you choose the theme, the icon appears on the layout. Once you have several icons added and you forget where the icons were located, you can switch back to 'classic' theme to see what the original buttons were that you replaced with icons. Then switch back to your theme.
Lastly, you need to make sure you upload your theme to box.net, download the theme from box.net to your ipad. Then you need to go in through the edit function on the ipad and assign the theme you want to use for that layout. Works great once you get it figured out and easily makes the layout a more customized look and feel.
Hope this helps your cause.
