For each project that you link to BIM 360, you need to specify the Project Files subfolder where it will upload the PDFs.

For example, if you specify "Subcontractors/ACME Contracting", then your Damstra Forms PDFs will be uploaded to "Project Files/Subcontractors/ACME Contracting".

Note that if you are running a restricted integration, your BIM 360 Integration User must be granted "View/Download+Upload+Edit" permission for the subfolder.