If you have live plants planted in the substrate, make sure to only vacuum twice a month as the plants will use the waste as fertilizer :)
Usually you just siphon around the decorations.. you can remove the fake decorations (leave the live plants in) if you wish, but not necessary. If it makes it easier to siphon, then by all means remove them.
Here is what I did for all those years I had substrate in my tanks (don't miss having it now! With hours of water changes already, not having to deal with siphoning a substrate really is nice lol) -
Fill the hose with water, cover both ends with fingers/palm of hand(s), place one end in tank, the other in bucket.
For motion I tended to go up and down moving around the tank - place the end into the gravel an inch or three (depending upon depth) then pretty much immediately lift it up to right above the top of the gravel line and let the gravel fall on it's own while the waste is being suctioned out. If the tank is smaller and I don't want to remove too much water then I'll go around and pick spots sort of close to one another rather than siphoning every inch. I move it quickly, so you don't have to wait until every piece of gravel settles.. sometimes I have a fair amount of gravel still in the tube when I move to the next spot. As long as you don't let it get jammed or to the point you stop sucking up new gravel then you don't have to wait.
Better yet.. a visual.. lol -
Brown = gravel
Green stars = plants/decoration
White circles = siphoning locations
As you can see, not every inch is siphoned. Large tanks you can get away with doing that.. or you can use a smaller siphon to remove the water more slowly (but it's tedious work). Siphoning randomly and in key areas (like where the fish hang out the most at) works just fine - as the next time you siphon it won't always be in the exact same spots.
Last edited by Myates; 05-07-2013 at 08:20 AM.