Sam3 and Sam4 share a very similar ADC controller, and I suspect that Sam4 datasheet is more up to date.
See table 42_4 page 1093 of Sam4 datasheet. It is stated that in differential mode, CH6 - CH7 = CH3.
And in fact, I did test it, if you enable channel 3 in differrential mode, with analog inputs ONLY in channels 6 and 7, you will read (something) in channel 3 , whilst there is no direct analog input in channel 3.
I guess something is still missing, but this should be a right track.
I have found how to subtract 2 input values thru the fully differential mode.
Below is a snippet with a minimal code to demonstrate that it works. Note that OFFSET is mandatory, as well as ANACH bit to 1 ( except if ch0 and ch1 are already in differential mode) and of course DIFF bits accordingly. The subtract result is available in ADC->ADC_LCDR.