I've tried to make the updating process as simple as possible.
When an update is announced either on the Automatron forum or via email. You will need to download the new zip file containing the new version. You will be provided that link at the time of the announcement.
1. Unzip the new version somewhere on your hard drive.
2. In the 3dsmax#/Automatron directory, rename the AutomaScripts directory to AutomaScriptsX.
3. If 3dsMax is running and you have an Automatron scene loaded, please close the Automatron Panel.
4. Copy the new AutomaScripts directory into the 3dsmax#/Automatron directory.
5. Re-launch Automatron. Done! IF Automatron launches correctly, you may delete the AutomaScriptsX Directory.
6. Make sure you grab the new Automatron Help File from the zip file as this document is often updated.
7. Sometimes, there are also new user files such as BotAnimations, SnapShot Libraries and WalkaLoops provided with the Updates. These can be copied over to the appropriate directories if you choose.