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You can basically do it any way you want...most of the bacteria is in the filter and on the plants or anything that gets current. Bacteria isn't going to chill where it's being starved or resources, so it's not at all evenly distributed throughout the tank. And any bacteria that you pull out of the bed is usually with it's very own chunk of poop, so there's no net change.
You can clean the gravel however works for you.
When I had my turtle in my tropical community, I would do a FULL gravel cleaning with every weekly water change. I changed a lot of water (18 gallons or so), so I had the time to clean it all. The tank never re-cycled or anything.
Fish don't poop nearly as much as a turtle, so you don't need to clean the gravel as thoroughly. I don't want to mess up my decorations, so I just jab at the surface to agitate the stones (never pushing INTO the stones), then hold it until I see it stop pulling debris up...then move on.
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