When you install, you can just modify the path name of the installation directory. The installer will not delete any files (it will of course overwrite existing ones), so after this procedure, all your extra plugins will still be available.
In the future we will likely make plugins install in the user home directory instead of the program directory, and then this will take care of itself (almost, at least... we will need to consider version compatibility).
At the current moment, each release of ATK is a rather major upgrade. In the future we expect that new versions will be more incremental.
