If I wanted to transpose a group of MIDI notes up or down, doing so will also move the MIDI notes that are performing key switch functions for my sample instruments. This is obviously not a good thing since I'd have to move all of those notes back to their correct places. Is there a way to mark these notes as keyswitches so that Sonar will ignore them when transposing?  

You could put them in their own lane of the track, and lock the clip. Or just select limited note ranges in the PRV or use Select > By Filter to avoid them.

I often create a separate track for keyswitches. That way I can ignore them when working on the track.

That's a good idea, dranck.    Like the OP, I find many problems from keyswitches, transpose being a big one, and inability to use 'lookback' when play starts midway.  
 
So then do you have both midi tracks going to the same midi port & channel?  Any problems from that part of it? 

williamcopper
That's a good idea, dranck.    Like the OP, I find many problems from keyswitches, transpose being a big one, and inability to use 'lookback' when play starts midway.  
 
So then do you have both midi tracks going to the same midi port & channel?  Any problems from that part of it? 

that's exactly what I do, send both tracks to the same MIDI port and channel and just don't transpose the track with the keyswitches.
 
I didn't think about putting them in a track lane and locking the clip, tho, that's a good tip, brundlefly.

William, that is exactly what I do. No problems with 2 tracks having the same output. You can also use a different color for the key switch track too. Then its easy to distinguish in the PRV.

To help with starting playback, I add key switches at every marker that I might use to start playback from. It ensures the right articulation plays. Annoying but it works for me.

I program my key switches to be lower than my 88 note midi controller (mainly so I don't accidentally hit them during a recording).  So when i want to transpose I head to Piano Roll View and with the smart tool grab all the live notes and xpose.  The key switches are easy to avoid cause they are so low on the graph.
 
I use a Korg micro keyboard i have placed under my monitor to play the key switches.  I try to program all the key switches to be the same, so for example F-1 is legato in all the different libraries.
 
I like the idea of using a separate track and color coding it.
 
I used to have the Select>By Filter that brundlefly suggested programed with a keybind that worked well. Not sure why/when I stopped using that.
   

DRanck
I often create a separate track for keyswitches. That way I can ignore them when working on the track.

Same here. I can hide the keyswitches if I want, or hide the notes and only see keyswitches. The latter can be handy when editing multiple tracks and one track's keyswitches overlap another track's notes.
 
It also allows me to transpose the keyswitch track independently when the distance between the lowest note and highest keyswitch is too large to conveniently display both in the PRV. 

Jimbo, I like the idea of a separate controller for key switches. Sounds like a useful tip!

I put all of my keyswitches into a drum map