You'll need to locate the Machinarium.sol file.
For Mac users, the file path is:
{YourHomeFolder}/Library/Preferences/Macromedia/Flash Player/#SharedObjects/{RandomSequenceOfLettersAndNumbers}/localhost/
{PathToYourMachinariumInstallDirectory}/Machinarium.app/Machinarium.sol
For Mac Steam, the file path is:
{YourHomeFolder}/Library/Preferences/Macromedia/Flash Player/#SharedObjects/{RandomSequenceOfLettersAndNumbers}/localhost/
Users/{YourHomeFolder}/Library/Application Support/Steam/SteamApps/common/machinarium/Machinarium.app/Machinarium.sol
Note that the user's Library folder is hidden from view by default in Mac OS X Lion. If you're using Lion, this link will tell you how to find it (or unhide it):
http://reviews.cnet.com/8301-13727_7-20082044-263/os-x-lion-where-did-my-library-go/1. Once you've navigated to the Machinarium.app* file that is nested within your localhost folder, you will need to control-click on it and then choose "Show Package Contents" in order to see the hidden/invisible Machinarium.sol file.
2. Simply replace the Machinarium.sol file with the one that you've downloaded and you'll be all set.
* Note that this is separate from the Machinarium application that's in your Machinarium folder.
Also, for those who might not be aware, Mac OS X comes factory-set to hide most file name extensions, so you'll only be seeing the .app file name extension if you've chosen Finder→Preferences and turned on "Show all file extensions."