The approach I took personally was to create a custom template called style.css or whatever and then I added that to the list of css files that the headinclude template calls (there's a line with about 10 different css files being listed and I just added my custom one to the end of that).
Means that all my additions are in a separate template and means the difference between the original template and my own will be minimal making the upgrade process easier. In the past I used to spend ages comparing template versions to put that the changes I had made into the latest versions of the templates. So doing things this way means that will happen less often.
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