It's not a good idea to create extra attribute to store just the partnumber. Making the WTPart numbering schema manually do not require much efforts. Also it would maintain uniformity between you cad models and associated WTPart if you could choose the same number for both.
It's a basic principal of PLM even Windchill people recommends to follow.
If you manage your association between the cad docs and the WTPart smartly and choose appropriate link between them the second bullet you mentioned would no more problem.