I can't see why using a single molex would be a problem, as long as the wire gauge is sufficient and the power supply is up to the job. But if you find that you're having problems running it on one molex (it would probably have to be a pretty big load... exceeding the capacity of the +12v rail), then going with two or even three wouldn't be a bad idea.
If using two connectors from the PSU, you would still use a single toggle switch for ignition, since that's a seperate +12V going to the IGN/ACC input of the OPUS. Remember, the +12v going to the +BATT is the juice from the battery (which is technically always on), and the +12v going to the IGN/ACC is coming from the ignition (which only supplies the voltage when the car is running).
I don't see the need for an additional fuse between the PSU and the OPUS either, since the inputs are already protected with the onboard 25A blade fuse on the OPUS.