Ah, yes, the confusion that plagues a single user OS when he first starts running a multi-user OS.
Traditionally, root is only logged into to do administration. This is because he has full access to everything, and it is really easy to make mistakes, even if you know what you are doing.
I also suggest that you keep root near its default configuration, so that everything runs ultra stable, as root is often times a first place to stop when you can't solve a problem under your own login.
With that said, it is a much better idea, to always log in to your user account to do day to day stuff. That way, you can be sure that you don't inadvertandly mess things up. You can also just scrap that user account if you mess it up too much.
There are really many reasons why you shouldn't be logged in as root. Besides, your main user, the one you created at install time, should have really good access to most things. If there are things that your missing access to, you could always chmod the directory and files.
