well, the idea is to use dedicated sources (such as a DAC or a turntable) connected directly to the preamp or integrated. In this situation, the Marantz processor would be "just another source". You would use the Marantz as the master preamp when doing movies that require 5 channel audio. In this situation, the left/right outputs of the Marantz would connect to the left/right inputs of the integrated (or preamp + amp). The preamp/integrated would act as a "pass through" audio connection.
When listening to 2-channel audio, the Marantz would be completely shutdown. The Integrated would be switched to another input, such as a dedicated DAC. This would, theoretically, give you better sound quality because the goal would be to use a better preamp than what is in the Marantz. In my humble opinion, I don't think the Marantz is really that bad because they use discrete HDAM analog circuits (instead of preamps). I would also make the assumption that the preamp in the Marantz is better than the preamp in the Parasound Halo Integrated. The Parasound integrated uses the same preamp circuit as the Parasound P5, which is based on op amps. It's not bad, but there are definitely better preamps.