I suppose where the problem is; if you want to override the original theme files, you need to create a directory with the original theme name and add a suffix to it, for example:
If your original theme is a fiesta, create the fiesta-1629 directory and add here the files you want to overrides e.g. index.hbs. When you want to override the partials files, create a partials folder in the fiesta-1629 directory and then create a copy of the top.hbs file within that.
Do you appreciate the support you've received today? If so, consider donating to the Publii team by clicking here; we'll be sure to use your donation to make Publii even better!