Here i wrote a highly scientific answer to your cootie question then pushed the wrong button and erased the whole thing.
So to begin again, a cootie was originally thought to be a passenger on an unpopular child during the 1940s. Many of us in grade school at that time had lots of cooties. Later, as we became manure individuals through a very, very slow progression of misunderstandings and follies, some of us came to realize that cooties are actually the beneficial and not so beneficial bacteria and other small creatures living in the substrates of many aquariums. Thus it was that cootie became a highly regarded technical word. I have personally, though not intentionally, ingested many aquarium bottom water cootie cocktails while trying to start a syphon the old fashion way.
But enough science. If you plunge the syphon pickup directly into the gravel substrate, it should just suck up a few ugly cooties and not the gravel while not making a mess unless you spill. Of course, you should leave the interior of one half or more of the gravel undisturbed during any one partial water change. This makes sure you still have a good cootie culture.
