Thanks for the quick reply!
I've basically been doing what you're saying, Edwards, and it still has the large circle template:
I created a new black and white image in a paint program (Pixen), saved it as template.png, replaced the circle template in folder aquariatemplate/maptemplate with the one I created.
Ran Aquaria, selected mod "Template Mod", pressed tab to get the editor, selected "load level", typed in "template", selected "regen rock from maptemplate". Result: Still a circle.

I've even put the large circle template in the trash and it still manages to load it instead of my own new template. Very frustrating.
Another thing I tried: Modified the mod-icon for one of the already available mods (the test map) and there was no change in the image.
I am guessing the changes won't take effect until the game is reset or reinstalled but I don't know how that would work and I do not want to lose my saved games. Does the _mods folder need to be moved somewhere else instead of in the "resources/macinstall" folder?