I would rather have it all in one as long as it is a big tank. I always have had a tough time getting enough liquid into the black tank to get it to behave correctly. The exact problems I had due to insufficient liquid along with the solid waste is something I would rather not get into specifically, for both of our sakes.
I am sure there is a way to plumb it to keep the tank from backing up into the shower, putting the toilet lower than the shower is the first thing that comes to mind.
When it was all in one like on my truck camper I never had a problem, plenty of grey water to flush everything right out in one quick pull of the valve.
Chas