The config file (and by extension your registration data) is tied to a number of factors, including the location of the VoiceAttack executable, so you'll need to both register that installation and set up the options to match your other installation.
Registering the second installation on the same machine should not be an issue. It is not possible to run both simultaneously anyway.
Do note that by default all installations of VoiceAttack on the same user account will use the same profile database, so if you make changes or especially add actions that are only available in the beta version, that can potentially cause issues in the release version.
There is an advanced option for using a different profile database, should you want to make absolutely sure nothing will conflict between installations (search VoiceAttackHelp.pdf for "-datadir" for more information).