If I were you, I'd clone the common/style.css to a new file, make changes to the Jplayer CSS in the new version, and point to it instead of the original in your skin's style.config. This way your changes wouldn't get overridden by upgrades. You'll just need to avoid changing any of the CSS in there that doesn't relate to Jplayer, and during upgrades you'd want to compare your customized version to the delivered one so you could take advantage of any non-Jplayer CSS changes in the file.
Since it sounds like there are different themes for Jplayer, maybe the ultimate solution would be to have mojoPortal deliver the Jplayer CSS within its own standalone CSS file (like we did for Colorbox), rather than lumped in with other common styling? It sounds like that would make customization of this CSS simpler and safer, if Joe is amenable to making that change.