I just stumbled across the alignment feature of Astroplanner (v2 beta). In the "Telescope" menu there's a "1-star Polar Alignment", "Iterative Polar Alignment", and a "Polar Drift Alignment Helper".
By default it installs itself in a different directory anyway. v1.6 was something like c:\astroplanner, but v2b is c:\program files\astroplanner I think. So keeping them separate is not too hard, and they're different icons too so easy to distinguish them.