If I understand what you're trying to do correctly, you will just have to make the changes on the default files after you download them. Then when installing a new file, you would just upload these modified files and the pages should be branded already.
As for uploading the files after testing locally, you should keep the relative paths the same. You may have to update the connections file for the database on your server. As always, if you run into any issues while moving the files, you can always post here in the forums and we'll give you any help we can with it.