I was wondering, if you were playing say a 500 point game and use used 400 points for the rookie version of the big Phoenix and another 100 points on various x-men characters, is it possible to transfer clix from the various clix to heal Phoenix past her starting point?

No. You can never heal a character past its starting point.

But the starting point isn't exactly a starting point for the big fig if I were playing at 400 points. Usually big fig rules prevent support from working on them hence there has not been a similar problem, but in this case the starting point is already 6 clicks down the dial.

It is her starting point. Check the dial. See that little "R" in a circle between the DV and damage? That indicates the starting position for the 400 point Phoenix.

Ah, I never noticed that. I've been looking at the Wizkids site the whole time