Actually, no WAS does not use the VAJ Persistence Builder for its CMP. The container implementations are totally different -- it's just that the tools are similar in V 3.5 and previous...
My advice is to use WSAD 4.0 to map to your tables. Failing that, the best way to learn about how the all-important XML binding files work in WAS 4.0 is to read my articles
here and
here Kyle