Caitlyn,
Thank you for asking these questions. A how-to response is the kind of thing I would like to see in Cayuse's user help section for everyone's access. But, allow me to tell you how I'm planning to do it. And I know others have their approaches.
I haven't yet had the opportunity to actually share my institution's documents, but I've been thinking about it as I prepare the program description for an AAALAC site visit.
I have already made a blank protocol application by entering the very minimum amount of information (some words, spaces, and boxes checked) to satisfy "completion" of a section and to create a full example of the protocol. I did this in the STG (training) environment, not in PRODuction. Because the structure of the template is the same in both, I haven't used up a protocol number in PROD.
For protocols which an agency might want to review and "inspect", a PDF can be created after clicking the preview tab in the image below. The PDFs can be made available to the team electronically. During the restrictions of COVID, I did a few AAALAC site visits; each institution created a Dropbox or Box account for us, which contained SOPs, protocols, training records, etc. for our perusal.
Does this help?
Bruce