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.