From what I have been told... Cleaning the sand first is the best idea. I think rinsing it would be a good start....
As for care of sand... I've heard both sides. "The sand makes my water murky" and "It's the best!"
To get gravel out is a pain in the butt, I would know!
You could drain, it would make it easier. Beneficial bacteria does not float about in the water, but rather is on the walls of the tank, ornaments, the filter cartridge... So, sit the objects, plants, and filter in water to avoid it from drying out and losing the bacteria.
I think some people use oany hose on the end of their gravel siphon to clean the sand. For me, kink the hose or put my thumb over the end to keep the substrate from being sucked up (gravel tend to get stuck lol)