Thanks, I dont understand what you mean by "double MCU model" but I think I got it working although I'm sure a lo of what I did was irrelevant.
I created two power terinals and in power rail config I created two net classes and then allocated them on the power rails tab, now if I create a PCB layout I get no errors and everything seems to be properly connected. Also as HackandCrack posted change hidden pins in any affected models. I also buggered about changing things to experiment so maybe there is something I've forgotten. I'll go thro the process from scratch and document a "How to" for anyone who finds this thread helpfull.
Sorry, I mean double click MCU model.