I bought a 5 subject spiral notebook, because I have 5 classes.  Each section for a different class.  This keeps it simple.  All of my notes are in one notebook.  
If we have had a test over the material, I skip a page in that section then write "Test 2" at the top of the new material section that is supposed to be for the second test.  That way I don't get it confused with the information that I have already been tested over and dont need.
For loose papers, I just keep them in folders.  Usually, 1 folder for 2 subjects.
Time management: this does vary from person to person.  I don't spend huge amounts of time on schoolwork.  I don't believe in that personally because you have to have a life too.  I do break up studying and homework into short 30 minute sessions.  I do homework at werid times too.  I don't really need to put aside time to do it on most occasions.  when I get a few minutes here and there, I make sure I have my books with me so I can just pull them out and start working.  I do this between classes or when I'm waiting to meet with a teacher.
In some cases, you may just have to force yourself to open the books.  Once you get started though, it's not as terrible as you think.