There is no "this is how a site should be set up", as that will differ per community.
However, I tend to leave absolutely everybody in the Registered group, use Registered to assign default permissions, and then only assign any permissions that differ from those to the relevant groups. This greatly reduces the amount of work required to get things setup.
Worst case, for a total reset, hit the "Not Set (No)" button at the top to reset all permissions for all individual groups, and then reassign the rights starting with Registered, and working your way onward from there. Turn off your board before you do, though, as the reset will mean permissions will seem even more screwed up while you work).