You will have to run both the grounds as on eis a 5v and the other a 12v ground.
Depends on how far you want to go with this, if you really do not want any cables between the PC and rad box, you could purchase one of the new flow meters which has a USB connection on it, you can then connect that to your motherboard and set an alarm to shut down your PC if ther is no flow. However without a USB connection to your aquaero in the radbox you will not be able to monitor/control anything with the software. If you are going to run a USB connection to the radbox you might as well but a nice piece of flexible round conduit and run all the cables in that. You could always even use coloured tubing to match the watersooling tubing and run the cables in that so everything matches.
Odd that the grounds are not common - I would have expected them to both be common with the AC mains ground, or at least common between the two of them? I have actually connected fans across red and yellow before on molex to get 7v, so surely the grounds must be common otherwise I couldn't rely on there being 7v between the two live rails?
I do plan on running USB to the radbox - I have an external->Internal USB cable here ready to go, along with some USB extensions (radbox hoses will be quite long) laying around that I can use for this. I have a flow meter that will connect to the flow meter header on the aquaero (the flow meter will be in the radbox). So my total cables to the radbox from the PC will be:
1. Molex power
2. ATX break
3. USB
I do plan on ATX break for failure modes, eg. no flow, low res level (got a tubemeter), water overheat etc.
No problem really with running however many cables are necessary, I just want to get it down to a minimum and plan it properly so I run only what is really needed.