If I use a custom skin, do I start from scratch or from existing skin files?

Either--whichever you prefer. When custom skinning is enabled in your account, you will be given access to an FTP folder containing the necessary skinning files. You can either modify files for existing standard skins or start with basic files to design your own skin from scratch.
You can view the skinning guidelines at https://presserolibrary.chi.v7.pressero.com//files/skins/docs/#/

If you are interested in enabling custom skinning in your account please submit a Pressero Support ticket.