If you are changing from root to user, you are changing ownership, not permissions. chown is the command.
Which files' ownership do you wish to change?
If you change ownership of all files from /, a lot of bad things will happen. Don't do it.
No matter how good the X system is in Linux, there are certain things I would prefer to do from a command line. That does not mean you cannot do it graphically, but I find it harder to do.
Here is a link that discusses permissions: