New JetPack CSS Feature? Advanced Questions

Hello Everyone,
WordPress has really been giving JetPack some attention. Overall, I love the JetPack suite. Here is my question though. I develop mainly on the Genesis Framework, and work with their child themes almost completely. Curretnly, when I edit the CSS of a theme, I kind just go to the bottom and add a /*** Custom Styles ***/ addendum at the end of the stylesheet. The problem with this is if the theme ever gets updated, I would lose the CSS changes I made (I obviously have MULTIPLE backups, so no data would really be lost). I want to know if it is considered “best practice” to edit this at the bottom of the style.css or do this some other way. I am partially concerned with page load speed, so I try to avoid things such as @import and the like.

Thanks for everyone’s help
Zach