I am a contributor on http://www.haxenme.org
, so I am trying to consolidate to make that the "source of truth" for how things work. Your feedback is very helpful, because I want to make sure to include enough documentation, tutorials and examples that no one has to feel stranded.
If you do run into specific questions or issues, the forums should be a good place where I or someone else will be able to help you.
The biggest change between these project templates (which are currently out-of-date) and the updated build process is that the packaging/build process used to be managed individually. Now, there is an installer tool which can handle it all automatically. Particularly for going cross-platform, that tool makes things much easier.
Here is another template which is more "bare bones," but when I have a chance I should create a true FlashDevelop project template (like these) which you can use to create new project files without editing names or references.http://joshuagranick.com/code/haxe/NMETemplate.zip
The difference between an application packaged with the NME install tool and one you can submit to an application store depends on which store you are targeting.
There is nothing more you need to do to submit your application to the webOS App Catalog. Just submit. For Android or iOS, you will need to include your own certificate (instead of an empty, dev certificate), but otherwise those packages are good to go as well.
If you want to publish on Facebook, the Mac App Store, Ubuntu Marketplace, Chrome App Store, or try for services like Steam or Desura, you will have to package for those stores. Lastly, if you want to publish to Blackberry App World for the Playbook, you will need to publish as Flash and then publish as AIR. Currently that is much slower than the native applications NME creates for iOS, webOS and Android, but I don't think (not sure) there is a solid C++ path for BlackBerry