No problem! Setup your project using the first PDF (or one of the PDFs). Then under Setup you can easily append additional PDFs (either the entire PDF or a subset of pages) to the existing project.
To append a new PDF to an existing project follow these steps:
1. Open the project in question and enter Setup
2. Tap Append
3. Select the PDF you would like to add
4. Tap Select to add the entire PDF or Partial to add some of the PDF pages.
The new PDF (or selected pages) will be added to the end of the existing PDF for this project. Your existing pieces will be fine, and you can now create new pieces from the new pages.