The 1.01 update was primarily designed to address game-breaking bugs and multiplayer stability issues that were present at launch.
Unzip the contents of the archive into your main game directory.
The version of Emergence sold on GOG.com already includes the 1.01 fixes and additional wrappers (like nGide) for modern displays.
This patch does not natively support 16:9 or 21:9 resolutions. You may need a community "Widescreen Fix" or "Camera Mod" in addition to v1.01.