When using the ThirdPersonTemplate if I replace SK_Mannequin with my imported iClone Char it no longer does the default animations. I have reassigned the AnimClass to the default third person blueprint. Are they not compatable?

You have to do skeleton retarget from mannequin to CC3 , or when importing choose the mannequin as skeleton , if you choose none it will create a new skeleton which has to be retarget.