Ideally, you should stick to Color Palette for the global color changes. From there you'll move to "Basic colors". These properties control the majority of the colors in XenForo styles, you can dramatically change the colors of the style by sticking to these two pages. To customize elements even further you may need to dive into the style properties or extra.less.
That being said... making color changes, in general, shouldn't involve you editing the main XenForo templates. Any additional CSS you want to be changed you can place inside the template: extra.less which will be preserved when you upgrade.