Hmmm. Never thought of that. Would be handy. But, as far as I know, there is no way to make folders in the Notes app - and I couldn't find anything in Cydia, either. Sorry.
Guess you'll have to use one of the note-taking or filing apps available in the App Store. I use Evernote as it is sync-able between my iPhone, iPad and computer. With it, I can make folders (a.k.a. notebooks) that go as deep in levels as I wish. Of course, there are many other apps, this is just what I use; I keep the Notes app for simple notes...
Marilyn