There are some comments near the top of the file that describe the format and range of values you're allowed to use for each <color> element. Be sure to read them carefully.
Beyond that, skip down a ways in the file until you find a <theme id="Synthesia Classic"> section. This is all there is to defining new themes. Add a new <theme> element after that one with some id (which is the name that will appear in Synthesia). You can then redefine as many or few of the existing top-level colors as you like.
One really easy way to reuse values (like a particular hue) in color themes is to use a <scalar> element. They only contain a single value, but that value can be reused as many times as you want. Here is one example:
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<scalar id="baseHue" value="200" />
<color id="someColor" hsv="baseHue, 70, 30" />
<color id="anotherColor" hsv="baseHue, 20, 60" />
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<color id="accentColor" hsv="baseHue + 180, 20, 60" />
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<theme id="My New Theme">
<scalar id="baseHue" value="20" />
</theme>