The templates in Papyrus Author are designed for specific output formats. They cover many of the most commonly used formats, although not every one. So yes, if you want the output to look different to the existing templates you will need to make the changes.
Yes, these are your two options. Once you have created the format you want, you can save it as template to use again. We discussed doing this in the thread Copy a ‘Blank Project’ Starter with Pinboard Populated.
Alternatively, once you have one project with the format you want, you could apply that to any other .pap file through the “Adopt Styles from Other Document” option. This was discussed in a previous thread Can I change the format and size of a project.
Both of these options mean you only have to make the format changes once, and not every time you create a new project.