Hello Jonas and welcome to the forum. I think you'll find Nisus Writer's interface much easier to use than Mellel's (and much more pleasurable). Mellel is a powerful word processor, but it has one hell of a learning curve. NWP is just as powerful, but as intuitive as the Mac itself and tends to work with you rather than against you.
First, when you save a document in Document Manager, it saves the file in the \Documents\Nisus Documents folder in your home directory.
Second, I was once like you as well, not really knowing how to incorporate Document Manager into my workflow. I once even stated that it was a "useless feature." Now, I couldn't live without it and it is one of my favorite features of NWP. So much so, I have set in the preferences for it to open when NWP opens, instead of the default new document.
Third, I use Document Manager as:
1. a place to hold aliases (shortcuts for you former Windows users) of all my documents that I'm currently working on. That way, I can easily open them when NWP starts and when I save them, they are saved in their original (and more permanent and logical) location (like a folder for the class whose lecture I'm working on) rather than in the physical Nisus Documents folder (although the alias remains there for easy opening).
2. a place to hold certain templates (like ones for class lectures, article templates, etc.). I have to use these a lot, and the Document Manager is a great place to keep them (rather than some Template folder that I would have to navigate to every time).
3. a place to quickly save something when I don't want to deal with the save as dialog (use File - Save in Document Manager, which I have shortcut'ed as Cmd-SDM) or I am pressed for time.
4. a place to save documents that really don't "fit" anywhere else in my permanent filing schema. For example, algorithms for Nisus macros...where do I file those, because I don't do enough of them to really have a separate folder? Well, the Document Manager maybe?
The one drawback of Document Manager is that you cannot determine what folder it points to (which would be useful for those who want to have it point to a folder on an external drive which moves between two or more machines with NWP/NWE installed). It is defaulted to /Documents/Nisus Documents in your User folder and will only work with that location. I get around this by placing an alias in my Work folder, which works like the document manager for my system but on a much larger scale--everything from syllabi in Pages to gradebooks in Numbers to lecture presentations in Keynote.
Hope this helps and feel free to ask questions.