Don't stress too much over the small amount of water in the filter, it is probably less than the volume of water in the gravel bed. Keeping the filter media moist is important but I never leave a filter or a tank empty long enough for my media to dry out. When I am doing a filter clean, as I finish with each part, I just stack it beside the sink and leave it there until I put the filter back together. I do not use running water to clean my filter but use the sink to catch all the spills that I have while sloshing the media around in a bucket. My canister does not get refilled before moving back into place, it is designed that way, so the media sits damp for 10 or 15 minutes each cleaning and I have never had that affect the biofilter function of one of my filters.