Yes, use the Override key to keep from sharing between. For sheeping I would do something like:

MageA Macros:
F1 (for example): /focus target
F2 : /target focus
/cast polymorph

MageB Macros:
F3 : /assist MageA
/focus target
F2 : /target focus
/cast polymorph

This is assuming MageA is your main window. Your procedure would be to have MageA's window up. Select his poly target and hit F1. Have him select MageB's poly target and hit F3. Then when you hit F2 both will poly their targets.

Personally I would go with two Frost mages and go for Shatter builds. With Frostbite on two mages you'll have an excellent chance of Freezing your targets.