to create a .deb file from .zip with YouRepo, you must respect the architecture of your device. For example you have a WinterBoard theme, "MyTheme.theme" folder, and you want to create a .deb file.
To start you must have your "MyTheme.theme" folder filled. And you want to place it in this folder on your device to work with WinterBoard:
This will require that you create a Library folder, inside a Themes folder where you put in your "MyTheme.theme" folder.
Finally you can select /Library and compress it.
If you want to add more tricks in an other folder than /Library, eg a widget, you must put your folder MyWidget.iWidget in:
You can select your /Library and /var to zip it, it is a precision to show than you can select multiple folders to make a zip =)
A simple tutorial is available on YouTube, thanks to Adam.