How you bring updates into your changes depends on where you make them:
The Marketplace installs each version of a module or skin in its own folder, such as skins/jrElastic2-release-2.1.2. The normal folder name, skins/jrElastic2, is a symlink to the newest version. So the server can hold several versions, but only one is used.
That makes it hard to see what changed in version control: each update is a new folder.
Developer Tools has Rebase Skins and Rebase Modules tools. They move the newest version back into the normal folder and remove the symlink, and can delete the old versions. In version control, an update then shows as changes to the same files.
To show these tools, turn on Enable Reset Tools in Developer Tools' Global Config. They're then under Tools.
Rebasing changes folders on the server. Back up your site first, and don't run it on a live site you can't restore.
If you build in files, clone the skin first (Cloning a Skin) and keep the clone in version control. Then compare it with each new version of the original, with Compare or your own diff tool.