Skimmer questions

Many tanks use neither a skimmer or a filter. Instead, they rely on water changes and the natural bio-filration capabilities of the live rock placed in the tank. It can be easier to be sucessful running skimmerless in smaller tanks (the higher frequency of water changes takes less time in smaller tanks and is easier to keep up with), but there are people that do not run skimmers on larger tanks as well.

If I put a skimmer on the intake of a filter, would the middle and bottom of my aquarium still get filtered or would the skimmer only allow it to filter the top of the water now?

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I'm not sure I understand exactly what's being asked here... If you're referring to a surface skimmer, like those designed for canister filter intakes, that is different than a protein skimmer. The type intended for a canister filter intake pulls water from the top of the water column (but not exclusively from the top of the water column if I remember correctly), which helps to eliminate / prevent any sort of organic film on top of the water. It only pulls the organics that are trying to settle on top of the water off the top of the water, it doesn't actually remove them from the water. That would require heavy carbon use, or an actual protein skimmer.

Protein skimmers are not particularly quiet, at least not quiet enough that I would want one running in my bedroom. Newer, pricier models are coming with silencers on the air intakes, which is suppose to help make them more quiet. Besides the sound of the skimmer drawing in air, it's only as quiet as the pump supplying water to it. They do also splash a little water from the water outlet, which can be noisy depending on the design and how high the water outlet is from the top of the water.