In an ideal world, you would use the MH for Veg, and the HPS for Flowering. That is a serious amount of light to not use it, so if you haven't thought about tossing the 1000Watt HPS in your flowering room, then think about it for sure.
Personally, I like the MH simply because it produces fuller plants, which can lead to more budding sites. If you are doing a continuous harvest, your best bet would be a MH in Veg for smaller plants, and the HPS hitting homeruns for you in the Flowering room.