They use DNA, and fossil records of the skin/feathers, as well as the skeleton. They also guess based on present day physical attributes/habits/noises/evolutionary traits etc. of their closest living relatives. That helps them determine coloring, and habitats, which helps determine other physical attributes, and so on. They get as much information about the animal first, and then they form a picture from all of it. It’s not just the skeleton.
Sometimes the fleshy bits make markings on the bones that can indicate their composition and structure.
Sometimes the fossil itself will contain the equivalent of a fossilized wattle or feathers.
Otherwise, they just guess based on similar animals, either in the fossil record where there might be more info on soft tissues or from current analogues.
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