Currently there is no good way of upgrading the theme without doing a bit of manual work. The future looks promising with [**gem based themes**](https://github.com/jekyll/jekyll/pull/4595) on the horizon, but for now here's some suggestions on how handle theme updates.
If you want to get the most out of the Jekyll + GitHub Pages workflow, then you'll need to utilize Git. To pull down theme updates you must first ensure there's an upstream remote. If you forked the theme's repo then you're likely good to go.
Depending on the amount of customizations you've made after forking, there's likely to be merge conflicts. Work through any conflicting files Git flags, stagging the changes you wish to keep, and then commit them.
Another way of dealing with updates is [downloading the theme]({{ site.gh_repo }}/archive/master.zip) --- replacing your layouts, includes, and assets with the newer ones manually. To be sure that you don't miss any changes it's probably a good idea to review the theme's [commit history]({{ site.gh_repo }}/commits/master) to see what's changed since.