Im big on over flushing, I like to put lots of extra water through it before I cap it off and refill. Make sure to use distilled water, not just bottled water, distilled water is much safer on your system then bottled(read: minerals added for taste)
When your doing you final fill I also like to add a quart of redlines water wetter, its a non glycol conditioner that they say can lower temps up to 30 degrees. While some would say its snake oil it makes me feel better about running a hot engine in sunny southern California.
Slow is Smooth > Smooth is Fast