Yes you can manage that through your cd_broker_conf.xml by assigning appropriate binding. Please take note of the following from the R5.3 SP1 manual regarding what all you can store on FS and what all you can store on DB:
For further details, I would recommend you to go thorugh the Content Delivery Implementation Guide that you can download from SDL Tridion World.
May be if you can zero down your requirement and paste your Broker Configuration File, the community can better help you :)
By the way, you can add another
Publication node in the Parent
Publications node with its id and defining Defaults Binding and even specific bindings for items in this publication.