The Prophet 12 and the module operate exactly the same way, the only difference being you move a knob in the section to make it active.
So for example if you wish to see the filter envelop settings you'll have to move either the attack, decay, sustain or release pot in the filter section for the info to be displayed. You can then use the soft knobs and buttons above and below the display to alter values exactly as you would on the module.
I have both the Rev2 and the Prophet 12 and they are both excellent, however in terms of navigating the UI, the Prophet 12 is MUCH better thanks to the bigger display and the soft Knobs and buttons that surround it.
Plus the numeric keypad (not found on the P12 module) helps too.
From a playing point of view the Prophet 12 is better too, largely because of the 'playlist' mode (which is very handy when playing live) and the slider strips which are just ace.
From a keybed point of view though, the REV2 is definitely better.
The action is very light on the Prophet 12 and it is very easy to accidentally trigger aftertouch just through normal play as a result, whereas on the REV2 you have to actually give the key an extra push to trigger aftertouch as you'd expect.
I've adapted my playing on the P12 now, so it's much less of an issue, but it's the first synth I've ever had to change my playing style for, so I think it's fair to say that this is it's only weakness IMO.
If Dave Smith were to offer a replacement keybed based on the REV2 for the P12, I definitely go for it.
That said, overall as an instrument, the P12 is definitely 'the daddy' IMO and by far my favourite synth in my arsenal.