The scaffolding is currently designed to give you a good start for building an application, but it does not build out the case for establishing relationships between existing entities (it does for GWT, but not for other UI types yet).
Your next step then would be to build a drop down component or other kind of “picker” for your existing children objects, and then modify the save handler for the parent object to refetch the existing child from the child DAO and then add the child to the parent’s relationship.
Let me know which UI technology (Flex, MVC, etc) you are using and if you need additional assistance.
Thanks,
Jack