I had problems making the layered images - when I put them together all the land or all the sea would turn black. I eventually worked out that it was because I was in indexed mode rather than RBG. Could be worth a note?
EDIT: just found a much bigger problem - when I'm saving images from the online mapper, they come out at different sizes so they don't overlay properly.
EDIT2: ok solved that. The problem was, the first time I updated the layers on the online mapper, it reloaded and changed the zoom slightly. Just had to remember to change then change back before saving the first image.