Ben,
If the association between Parent and Child is 1:M, you need to set the association value on each Child. If the association is M:M, you can set the value on either entity (i.e. if its M:M, you can set the association to a List from the Parent and/or the Child depending on how you set up the association. For an association owned by the Parent, you need to set the association value from the Parent, if its owned by both, you can set the value from either entity). BTW, you set the owner in the properties window of the association as highlighted below:
Let me know if you need any more info.
Mike