Download the new installer and run it. All of your profiles, settings, songs, and other custom content will be kept, but if you want to be safe, feel free to back those up or move them elsewhere before updating, and put them back afterwards.
For typical installs the installer will automatically update your existing installation. For portable installs, you will need to point the installer to your existing installation manually by entering the file path for it.
Delete the Clone Hero app and extract the new version.
Delete the following files and folders:
Then extract the new files into the game folder.
Download and run the new .apk. If you get an error about package incompatibility, you will need to uninstall the old version and install the new one. Be sure to back up your scores, profiles, settings, etc. beforehand, or else you will lose them!