When selecting an external image called "image_MAPPED.png", iolite will look for: "image_MAPPED.coord", "image.coord", "image_MAPPED.Coord", and "image.Coord" in the same folder as the selected image. If the image is just "image.png", it will look for "image.coord" and "image.Coord". If a match is found, it will attempt to load it, but may fail if the file contents are not as expected. If your naming scheme matches that described, send an example session and the png/coord files to support for me to have a look.
Regarding image ordering: I believe they are automatically sorted by mass and the external image has no mass causing it to be at the end. I can see how this is annoying for people that want a specific order in the overview, so I'll see about adding some features to keep the order and/or allow reordering and/or have an option to set where external images should show up.
All the best,