It should work in exactly the same way, even if you are playing from the healer.

You're right that the mouse is sync'd to the other windows, but it is sync'd to the mouse position on the main (that's the point) so if your main is the healer, the mouse must a;ready be correctly positioned. The way the bars are designed to work is that the mouse pointer is sync'd to be the same position on all windows and the heal macro is sent to the healer (by an ATG) with the target of mouseover (whatever the mouse pointer is currently hovering over).

Hope this clarifies things for you.