Hi Shal,
In my experience the best practice for associating documents to projects is to use the Document Manager feature in Clarity and store documents in the database. An exception would be a case where access to the documents is required for non-Clarity users. In those cases there isn't a best practice of which I am aware. The SharePoint link you refer to may not provide what you expect.
There seems to be some concern about the DB, but apart from the size I'm not aware of any problems MS DB may pose regarding the document storage.
Document Manager provides check-in, check-out, versioning, history, and security, as well as process automation and notification capabilities. The document security is in addition to Clarity user security and specific to each project. The document owner is primarily responsible for managing access to their documents. The Collaboration Manager(s) may also control document security for documents on the project to which they are a Collaboration Manager. In most cases the PM, Collaboration Manager, and document owner are one and the same so it isn't as complex as it may appear here.
Documents which are stored in the DB have the added feature of users being able to search for them using the Search/Advanced Search in Clarity.
Like so many features in Clarity training is key, followed closely by practice.
I hope this information is helpful.
Cheers,
Dan