Rhett asked, "What if I use Wordpad (which exists in the base) to create a .DOC file? Does SVS layer-ize files based on whether a layered program created them?"
Hi Rhett. If you create a file with an app that's running from the base, by default it gets written to the base. If the app running from the base modifies a file from an application layer, the new version goes to the base and the old version stays in the layer (this prevents an app in the base from potentially breaking a virtualized app -- we're assuming people are using data layers correctly and that this sort of a mod would be to a program or config file, which you don't want).
Best practice is to have everything in one or more data layer(s), so that it doesn't matter what app is doing the create/modify; data always stays isolated and out of the base (and not duplicated).