MariaKim
Exact same setup- uTrack 24, Kemper and a fair bit of other gear... not using Sonar (but there's no difference in the workflow for that really)- I haven't used Sonar in a *very long time*- but I recall it had some extremely powerful editing tools - especially for MIDI.
Important question though:
Why not Performance Mode?
Using performance mode lets me set up the stomps and settings per slot. For example, if the verses are clean + chorus and the choruses are dirty, I can pick a nice fender bassman and set it up JUST right with the chorus and other effects for the verse, and ... say a MesaBoogie or Marshall for the dirty stuff.
The patch changes are (I'm told) faster in performance mode too- there's no gap or switching delay. It might be the most accurate patch switch I've ever experienced, actually.
In performance mode, you can order your set list in Rig Manager, and then send CC#47 with a value of the performance number, then CC50 for slot 1, CC51 for slot 2, CC52 for slot 3 and so on. This way, you have 125 performances with *5 slots each* - much more than the 127 available in browse mode. You can also send PCs to select individual slots, but it requires bank switching in MIDI and it makes it a little harder to understand what's going on. With CC# changes I can look at the midi event list and see that I'm on performance number X and see where the slot changes are really easily.
On Transpose:
I have a few songs that are transposed DOWN a few steps - I just set the transpose in the rig itself (in performance mode) so when it's selected it's pitched down. Selecting that performance/slot takes care of the transposition.
(2) For the individual stomps, you can send a CC (continuous controller) message. I'm at work so I don't have all the CC#s handy - but they're in the manual under MIDI.
I don't use program changes any more at all - I just finished converting my (40? 50?) song set list to use CC#s.
Anyway- I'd be happy to compare notes or work through this with you. LMK.