What you're looking for is a topic called "Revision Control." At the moment, your best solution is to try Git.

http://git-scm.com/

The simplest thing to do is to setup a repo and put it on Google drive or drop box or something. That way you can access the code from home, school, on vacation, and you have an offsite backup. Of course putting your stuff online caries some risk of someone else stealing your code, but if you're just learning to code, that's not a concern.

I wish I had know about revision control when I was in school. One of the great things these systems do is keep track of changes and let you undo mistakes. This would have saved me countless hours in school when I broke something and couldn't get it working again.

Work through the manual, and just learn the command line. There are only a few commands that you'll use on a daily basis anyway.

http://git-scm.com/book/en/Getting-Started

For example, all I ever use is:

git checkout -b new-branch

git add --all

git commit -am 'commit message'

git stash

git stash pop

git merge --no-ff branch

git branch -d to-delete

And that list is for a company with tons of software. You won't event need all that!

I think the op meant how to organise it's files. Keeping them all in the same folder is usually a good idea, unless you have a very large number of classes, then separating them in folder would make more sense.