Multiple banks / patches in one Pentagon instance?

Pentagon is a great polyphonic mono-timbral synth.  The banks are used for organizing the presets into groups, but you can only load one sound at a time into an instance of a synth like this.  So you load a new instance of Pentagon on a new track for each different sound you need.  Then set it and leave it.  Soft synths are not really designed to work like external synths and respond to bank/patch change messages.
 
The alternative is to use a multi-timbral synth.  I believe that Cakewalk TTS-1 (GM) is the only true multi-timbral synth included with Sonar 8.  You can assign up to 16 different parts on this one.
 
Third party products like Kontakt, SampleTank. Garritan Aria. etc., are all multi-timbral, so that with one instance you can load sounds into each part and play them back via individual MIDI channels.  You will still need additional MIDI tracks routed to each respective channel part in the multi-timbral synth to control them.  You would need to set the sounds in the plugin, rather than with a bank/patch change from the MIDI track.

Sp3ctre18
Ah, mono-timbral, eh? So it's meant to be that way. Ok, thanks a lot. I thought I just didn't know how to use them.
 
What exactly do you mean when you say that Pentagon's banks are for organizing presets? Is it that, if I want to use multiple patches from Pentagon, I can set them all up from a single window and then open up the extra instances when ready? Because it does seem to work that way.

Patch banks is an old concept carried over from the hardware synth days. The idea of having 128 patches per bank (0-127) lent itself to creating instrument definitions that followed the MIDI patch/bank change messages.
 
Most modern soft synths have their own internal patch management systems, that do not reflect the historical way of organizing MIDI patch libraries.

Sp3ctre18
Well then, again, why does Pentagon I have 5 banks I can select and set, labeled A-E? I'm not seeing the point if it's mono-timbral. I think I remember some other synth that similarly had 2 banks?

Well, all I can say it's been around for years ... an oldie, but a goodie!!!  Read up on MIDI synths

Well I do wish you luck getting the sounds you need out of Pentagon! 
 
It can be a powerful synth in the right hands!  Not bad considering it has been around for over 15 years! 
 
Here is the Pentagon 1 user manual: https://www.cakewalk.com/Support/Knowledge-Base/2007012984/Where-can-I-download-the-Pentagon-1-manual
 
I went back to re-read your original questions, and made a few more observations:
 

So first things first: Trying to use Pentagon I in Sonar 8 Producer, there are patches loaded in to Banks A-F. How do I set up my tracks' output to play the right bank? They seems to only play whatever is currently in focus in Pentagon.
 
In the track, I have the right bank selected, the right patch, and I have no idea what to do about "channel," but trying omni, 1, or 2 made no difference.

 
To clear up any further confusion, my best suggestion for using soft synths with Sonar would be to stop trying to use the track settings to set the bank/patch in the plugin. Yes, Pentagon does respond to bank/patch change messages, but that gets messy.  That is a design carryover from the old days when we all used external hardware synths and the patches were all stored in outboard gear.  Cakewalk doesn't support instrument definitions for soft synths, and most soft synths of today don't follow the legacy bank/patch select methods, so there is really no standard for that now.
 
Instead, use the plugin GUI menus to set the synth to the sound you want to use.  In the case of Pentagon, the patches in Banks A-F are not loaded into the synth yet, rather they are just listed as available on your hard drive.  You can only load and use one sound at at a time.
 
Put each sound you need on a separate instance of Pentagon, as many as you need, on their own tracks.
 
The MIDI track channel output doesn't matter to a mono-timbral synth, such as Pentagon.
 
You can leave all tracks on omni, as the channel number relates to the input that the synth should respond to.  To audition one or more MIDI tracks from your controller just enable the "Input Echo" for the tracks you want to play.
 
Once you have it all setup, when you save your project, all the patch settings will be retained within the project.  Each instance of Pentagon, or whatever else you are using, will remember it's patch settings.  Save your entire studio with one click!