This was taken off line but here is the relevant piece to the response for those who have similar questions.
For your questions about Port A (PA0-7), you should be able to use them as you described because we are phasing out those options (setup 1,2 and 3) in the ADSmartIO so that you can get the flexibility you need with the IOs. You can choose to have any pin be a digital input or output. You can configure as inputs any Port A lines you wish to use as A/Ds. Be careful not to write a "1" to those bits, or you will enable the software pull-ups, which will affect your A/D signal.
See our forum topic 306 for more details on changes/revision to the ADSmartIO.