Hi, it's not easy to understand how A-PRO works. I'll explain what I know.
By default, the two ports send these data to your PC via the USB cable.
- Port 1: data that are generated when you play the black and white keyboard (i.e. note, velocity, aftertouch, etc.)
- Port 2: data that are generated when you press/turn/move the buttons/knobs/sliders
These ports can be used for different purposes depending on the user and the manual shows diagrams with explanation, but if you're just using your A-Pro with a DAW and want to control parameters of the program and the plugins in it, you don't need to worry much. For example, suppose you have a MIDI track, which uses a soft synth, and this soft synth has parameters (filter, decay, etc.) that, by default, respond to certain Control Change messages. Now, from the input pull-down menu on the MIDI track, what input device should you choose? If you choose "None (i.e. omni)" or "All Inputs > MIDI Omni," data from both the keyboard (notes, velocity, etc.) and the controller (control change messages, etc.) will come into this MIDI track when you play/tweak the keyboard/controllers. And, for example, if you want to use the S1 slider on your A-Pro hardware to control the volume fader of an effect bus, and if this S1 slider is programmed to transmit CC73, for example, to the DAW and if you program the volume fader of the effect bus to respond to CC73, you can successfully tweak the bus volume fader by moving the S1 slider on your A-800Pro. BUT, if one of the parameters of the soft synth on that MIDI track is programmed to respond to CC73 by default, that parameter will ALSO respond when you tweak the S1 slider. Because you only want the bus volume fader to move and don't want the parameter on the soft synth to move, it is logical to choose "A-PRO 1 > MIDI Omni" from the MIDI track's input pull-down menu.
The above is a general idea and should be applied to all daws, and I have tested it and confirmed the behavior in Sonar using Korg M1 VSTi. And this is why I THINK it is recommended by Roland to select "A-PRO 1 > MIDI Omni" from the pull-down.
But, FORTUNATELY, if you use Sonar's ACT (Active Controller Technology), this doesn't happen. ACT seem to block the data of Port 2 (controller data) to come into the track, and therefore you won't have the above issue even if you choose "None" or "All Inputs > MIDI Omni" as an input device (I have confirmed this with Roland tech support). So, you don't really need to worry about what input device to choose, although I still choose "A-PRO 1 > MIDI Omni," for no apparent reason. :-)
(btw, I also use Studio One and its Control Link system also prevents the above issue)
As for MIDI channels, you don't really need to worry either. My A-800Pro's MIDI channel is always "1" and there's no problem with me. But it depends on what you want to do, so if you experience any issue, please start a new thread or post here.
What might confuse you besides the two ports is the software prepared for A-Pro hardware. There are two and the first one is "A-Pro Editor," which is obviously to edit parameters of A-Pro (i.e. which button/knob/slider should send what message) and the second one is "A-Pro Control Surface Plugin for SONAR," which uses the above-mentioned ACT system to "better" control Sonar and plugins in it. So, there are two options (use ACT or not), and if you decide not to use ACT, the feature you will use to control the parameters of Sonar and plugins is "Remote Control" (it's explained in the Sonar Reference Guide). Whether you use this Remote Control or ACT is your choice. I, for some reason, combine both (which isn't recommended by Roland). There are advantages and disadvantages to both methods, but I first recommend using ACT, as recommended by the developer.
Finally I'll post some pics of recommended settings for A-PRO and ACT.
Hope that helps