Hi,
Automatic maps are re-created only when the post is published, and only if the checkbox ‘overwrite existing maps when saving’ is set on the MapPress settings screen. If that checkbox is set, manual changes will be overwritten each time you save/publish.
The custom icons filter and the poi template are only used when displaying a map (NOT when editing it or viewing it in the post editor). You’ll only see those functions when you preview a post, and you don’t need to re-publish to make them active.
If you’re previewing the post and not seeing them, try a simpler test – use just the template, or just the icons.
If you like, send or post a URL as well, so I can see if there’s a javascript error.