Hi @mrmattson
As suggested by Tony and others above, using Tags is a way to create virtual folder in Tiddlywiki. This is similar in what Gmail or similar software do. They do not have real folders, but use tags instead. In simple words, having a common property allow you to structure your notes (one note = one card = one tiddler in tiddlywiki).
You may also use Favorites Plugin: Update 4.6.8 - Discussion - Talk TW (tiddlywiki.org). It allows you to create two level structure in Tiddlywiki manually or semi-automatic.
Side note: you may also have a look to editions. See Mehregan, TZK, Stroll, and some starter editions in the Talk forum.