I have two 5.5 gallon tanks, a divided 10 gallon tank, and a 15 gallon guppy tank that and are (over) filtered and fully planted - they each get a 50% change on once a week and fertalizer the next day. I siphon out the water into a bucket and suck up any fish poop and other nasties, and while the water's low I work on the plants. When it comes time to put treated water back in, I set up the bucket on top of the tank and siphon the water back in to tank to help adjust the fish to any temperature changes in the new water (I get it as close to tank temp as possible, but there's some difference). All the fish stay in their repective tanks while I do the change.
As for cleaning the gravel with plants, you really don't
The plants suck up most of the stuff in the gravel bed; on occasion I'll gently siphon the top level of gravel on occasion, but the plants do most of the work. Sand's a bit different, though - unless you have Malasian Trumpet Snails, you need to disrupt the bed on a regular basis to prevent the formation of anerobic pockets.