Thats a huge task, and one that requires both an indepth knowledge of CNC and quite a bit of AS/400 knowledge as well.
In the System Administrators guide, there are lots and lots of steps that detail the installation of new datasources, new logic servers etc etc - as well as the configuration and use of JDBNet to do what you want it to do - but I think you'd be a LOT safer hiring someone in to reconfigure your CNC environment, especially since you want your new iSeries to be able to separately perform package installs AND you need to ensure that the data is being correctly backed up.
One thing to note, is that your central objects should ALWAYS reside on your main production server under Xe - or you should ensure that they are regularly backed up as if they were production data. Dev Central Objects IS production data, in my opinion, since you pay $$$ to have developers create your mods !