working in apache's document root
On Fedora or Ubuntu apache's documentroot is owned by root. Should I go in there as root and edit in this there? I don't like this, but I'm probably missing something.
No, I wouldn't recommend it, unless you only need to change something really quickly. Just use chown or chmod and give your non-root user privileges. Alternatively, you could make a symbolic link to a directory that you own. That's what I use for development.
I agree: you really shouldn't be editing files as "root", especially on a production system.
There are (at least) two good options:
1) Create a new group (e.g. "webadmin") and make your default document root owned by that group
2) Rely on virtualhosts, and secure each virtual host as appropriate: