My preference and what I generally saw when I was building my tank was that balancing the flow through 2 boxes can be challenging (but doable) where if you have one box you do not have to worry about balancing anything. Granted, this is only an issue if you are using one of the siphon style drain options (herbie or bean). The overflow weir length will determine your surface skimming ability and it really makes no difference if you have 1 box with 30" or 2 boxes with 15" each, so my preference would be the one large box.
I would highly recommend one box with 3 drains to start with (search BeanAnimal drain) as to my knowledge this is what most people wish they had if they have another setup. Basically, you will have 1 drain that stays dry (upturned elbow in my picture), 1 drain that functions as a duroso(ish) drain with low flow and one drain that is a full siphon regulated by a valve. The full siphon drain handles 90%+ of your flow leaving only a small amount in the open channel drain and the 3rd upturned elbow only handles water during an emergency if another pipe is clogged or during startup. In this setup you would have to have clogs in all 3 drains for the tank to overflow as both the open channel and emergency drain will for a full siphon if the water level rises. Some will probably say this drain setup is overkill on smaller tanks but after running it on my 120 I would not run anything else.
