Generally, yes, the overarching idea is that "Server" is the radio-less "coordinator." Therefore "server" would go on the hub where you plan on running the Apps that need visibility of the devices. Because it's bidirectional, technically it doesn't matter but.. at least here at the beginning, it sure would be easier to have similarity until the 'crowd' is large enough to experiment.
The radios are, in my opinion, the precious resource here. Of equal concern is 'bad reputation apps.' Ideally those would be as far apart as possible 
That's precisely what caused me to consider the three hub architecture. Having been running in a three hub scenario for several months, I continue to have had zero crashes. But my radio hubs are snappier in the big picture. There's simply more cpu cycles to manage the radio queue, it seems, without those bad ol' apps eating cpu. 
I originally posited that I'd be able to reduce down to a pair of hubs, once I better understood the load and exactly which apps were truly 'bad' in this architecture. The fact you wanted to start with two is great.
