Several comments:
Christian has noted elsewhere that he’s thinking about some different approaches for the root view. That may alleviate some problems and may show up in version 2.0.
The idea of a complete, un-grouped listing of all the documents in a database has been discussed. Remember that there’s already the History view, which lists all the documents in the collection, normally sorted by Age. In version 1.2 Christian has added the ability to add columns to the Tools > History view.
How to: With the History view frontmost, select View > Columns > option, e.g. Kind. Sorts of this flat view of the database can be made by several parameters, such as name, size or file type. As I’ve got about 20,000 documents in the database, I’ll probably not use most of those sorts. 
Tip: DT Pro will let one open multiple views of the top-level or a group view. And one view can be 3-panes, the other Vertical Split, or perhaps Collumns. The ability to look at the same complex of groups and documents in different ways can be useful sometimes.
Possibly useful tip: If you’ve got a selection made that seems to be interfering with your ability to “see” another group, or individual documents, Command-click on the selected item. Example: On my MacBook, the list of groups in a couple of my views extends below the screen and there’s no space "under’ the list to click on to clear the selection. Command-clicking solves that problem.
I don’t normally work in the 3-panes view, but I use it most of the time for my top-level view, as any “straggling” unclassified documents there are easily identified.
I also use the 3-panes view for my Incoming group, which usually has lots of unclassified stragglers. Sometimes I dump them in by the hundreds. I’ll probably never catch up. But I do try to classify new content as often as I find time. Sometimes I can move multiple related and selected items to an appropriate location. Sometimes I hit the Classify button to see if DT Pro can figure out where to put an item.
When I come across items for which I don’t have an existing group into which they would fit, I just create a new group in Incoming and add them there – worrying later about where to file the new groups. So I break the rule that a group should hold either documents or subgroups, but not both.