The way I use Evernote, as an example, is to have notebooks like a student in school, one for each major subject. Tags can go cross-notebooks, of course, so a note in the Math notebook could have "Test material" the same way a note in the English notebook could. I'm not a student but this way of looking at it helps me conceptualize it. I also have tags for year and month for various bills, lab reports, etc. If I get an electric bill I'll tag it "2012" and "04 - April" and "Bill" so I can search them all together if I need to see where my money went - a common occurrence lately
The downside to this approach is if I make my notebooks too detailed. "Medical" is fine, if I make one for "Doctor Visit", "Lab Report", "Bill", etc then I'll make myself crazier. Even if they are grouped into the same stack it's easier to not have to decide if this bill for a lab test goes under lab or bill!
The bottom line is, of course, that Evernote is flexible enough for each of us to do what works for us. Do what works for you and enjoy it instead of trying to fit into someone else's model.