In DNN 5 I would build the skin using the ascx method:
DotNetNuke ASCX Skinning for Professional SkinnersThe skin is therefore already installed and you can then use the same techniques from the tutorial to build the manifest file.
I am looking into skin widgets at the moment - currently experimenting with the new skin objects html method and the new super stylesheets, widgets will be after that.
I suspect that anything that needs installing before the skin such as skin objects and widgets will need to be placed at the top of the manifest file.
I'm guessing you could also place the module manifest in there as well. I don't think it will matter if the module is installed before or after the skin in the manifest.
Thanks,