In my case I edited the theme record directly as I didn't think that was something themebuilder supported directly. So I went to /sys_ux_theme.do?sys_id=31bf91ae07203010e03948f78ad30095&sysparm_record_target=sys_ux_theme&sysparm_record_row=17&sysparm_record_rows=23&sysparm_record_list=ORDERBYname

then I clicked on Colors which brought me to:
/sys_ux_style.do?sys_id=a197a38107b03010e03948f78ad30059

the links will be different for your custom theme but it should be same general idea.

In this case you are changing CSS variables. I don't believe there is a way in the left hand nav bar to change the CSS in another way like editing a value in UIB.