I've seen this done a lot of ways, but others might chime in on their preferred methods. What I normally suggest is to either create the content in Jive directly, since we're also a knowledge base... or as I've seen some do, connect Jive to the API of your authoring/creation tool. Each time you publish a new document, it'll cross-publish to Jive and populate as if it was created there in the first place. This will create a better experience for the end user as well, since they will then be able to find those documents via enterprise search or filtering.
Stephanie - I would absolutely avoid the HTML route and stick to straight Jive documents. As we have all seen, there are limitations to how much html the average user can do and you don't want to be in the business of publishing for them.
One thing to watch with the files, make sure they are uploading a pdf file. Occasionally, I see these posted as attachments, which is just bad. They really want that content to be indexed.
Regardless of which way they go, tell them to get a good handle on tags. It will help them to set up simple tiles for access.
Shutting down the old repository and moving to Jive is the best solution, but that is not always possible for a variety of reasons. Here is another recent thread somewhat related: Connecting an external community to content on a separate website
Helen Chen - To my knowledge both methods index the content inside the PDF. I agree that uploading a PDF vs attaching is the way to go for sure though.