Hi Prabhu,
According to the Configuration Guide for this release, "WAAS Central Manager version 5.1.1 can manage WAE devices that are running version 4.2.1 and later releases."
Creating custom device groups is also covered in the Configuration Guide for this release. You'll find that yes, it's possible to create different policy settings for each group. As far as your question about impact goes, if I understand your question correctly, as long as your custom policies are sound, I don't see that you'd experience an adverse impact.
Good luck!
Jason