If you create your skin directly as .ascx files (as I do), you can simply use FTP to move the skin files to the server. You only need to run through the upload/parsing process if you develop your skins as .html/.xml files. The parsing creates the required ascx files from the .html/.xml files.

As for "localized" vs. "portable": that's an option for the parsing process.
Basically, they differ in the way how file paths are handled: a portable skin resolves the paths at runtime by using the <% = SkinPath %> tag and can so be used in any portal, whereas a localized skin uses static paths. More about that can be found in the skinning guide (in the "Downloads" section). But as you create ascx files, you can decide that during development.