Like WordPress themes, each PMB design has different options. Some are flexible and have lots of options (eg the Classic Digital PDF for Digital PDFs and Classic Print PDF for Print-Ready PDFs) but others are more “opinionated” and have fewer options (eg the Buurma Whitepaper).
On this step you can choose those options, and save the design.
When you create another project and reuse the same design, you’ll also use the same customization options, and any changes made to the design will affect other projects using that design. This way the files you create will all have the same look, owing to them using the same design. So you should be able to customize the design once, and then on subsequent projects skip customizing the design (by just clicking “Save” at the bottom of the screen, without changing any of the options.)
Note: if your project uses multiple formats (e.g., both the Digital PDF and Print-Ready PDF file formats) you’ll choose the design for each format sequentially (e.g., first the Digital PDF’s design and then the Print-Ready PDF’s design).