There are several different places files can be uploaded if not created or received natively in Ambiki.

Evalution: In the evaluations section of the patient profile, you can create an evaluation internally in Ambiki, or upload an externally created evaluation
Physician Orders: Physician orders can be created within Ambiki's faxing system, or can be uploaded externally from the 'Physician Order' section of the patient profile
Assessments: Completed assessment protocol/books/testing can be uploaded to the 'Assessments' section. You can also upload these files directly into your evaluations if you wish. 
Uploaded Files: Each patient profile has an Uploaded Files section for various documents. You can upload PDFs, PNGs, videos, photos, and other multi-media