I'm not sure how you get new sand in there, maybe put the whole bag in there and cut just one side and pour it out on the bottom.
I don't think the sand storm is a big deal. it may be on the rocks and stuff for a day or so, but the flow and little creatures will make it fall on the bottom. When I used to vaccum the sand it would make a sand storm, but it never hurt anything.
one note is that if you are using south down you should rinse it prior to usage.
the turbo's don't seem to do it for me, thats great they are helping you though delsol