The stainless you refer to by the engine manifold is undoubtedly the heat shield, not the manifold itself which is cast into a plenum chamber rather than a 3 pipes into one set up that you might imagine. This has been a topic of some debate on oof as to how it affects performance and how an alternative design might tune the power curve.
With this in mind and the fact that the cats have oxygen sensors and wiring which will need terminating in a way that the ecu will understand to avoid error codes and a permanently lit dash light, i would consider sticking to a cat back system?
Boring and unadventurous as it may sound, its a safer bet imho. You can always go back when further solutions become clear, esp re manifolds, and join the system in the usual place.
As Kevin says i would be reluctant to alter the original design too much re boxs and routing without knowledge of shock wave scavenging,flow rates, and how annoyingly loud it will be on the motorway at constant revs. Although its nice to have v6 grumble when you boot it, that same roar is a right pain at cruising speeds. Some manufacturers use an exhaust valve to controle this noise to give the best of both worlds but this will require ecu input that the omega does not have.(i wonder if multi ram inputs could used for this?... The front one perhaps... No probably not )
You may also want to consider the rear end esp. the irmscher style twin pipe design which exits either side of the number plate, seen some pics of that box on here somewhere. Or simply a twin pipe exit on a single box as the elites.