Well, basically try to do everything you can as user. If you can't do something you want, see if there's a way to make it so you can. If you still can't, do it as root.
That's just a decent rule of thumb, but I mean 'see if there's a way' with some common sense - not to go chmod'ing everything world-writable.
The main thing to know is that most things can be configured for the user as the user in $HOME. If not, some things can be brought into $HOME. If not, it's probably time for root, though I've never seen any sense in not making my floppy mountable as user, for instance.
Another thing is that the need for root decreases. Once you've edited your fstab and started/stopped your services and so on - basic hardware and configuration stuff - there's little need to go messing with the machine or being root except to add or remove programs and check logs and so on.
I know what you mean about wanting to get it straight in advance (me too), but there's only so much of that you can do - the rest just comes from doing it.