Hi, Raymond - Really good question. You're right that the tracks as listed in the bounce window are not the same as the order in track view. And it doesn't matter if you've inserted tracks after the initial set up, or if you've dragged the tracks into a different order. Whatever logic there is to the order as displayed in the bounce window escapes me. It's not alphabetical or numerical.
But it's never been a problem for me. I'm so used to constantly adjusting the order of my tracks that doing that after bouncing (if needed) is just part of my work flow.
There's no confusion possible about what is on each bounced track if you've named your tracks before bouncing. For instance, if I have a Strad Solo track - the MIDI track has been named "Strad Solo" and the sample player audio track associated with it has also been re-named "Strad Solo." When I bounce, Sonar inserts the name of the project and the mix number, but also keeps the names I've typed in, so the newly bounced track will have this for a name:
MyMagnumOpus, Strad Solo, Mix (69)
After bouncing I routinely highlight the names of those tracks and simplify them - in this case, naming the track Strad Solo.
The Track Manager is of major help in keeping your project organized on the screen. You can access it either by pushing "M" on your computer keyboard, or finding and clicking the Track Manager icon in your tool bar (if you have its tool bar activated.) You will be shown the entire list of all tracks in the project, MIDI and Audio. There are boxes next to the tracks on the left hand side. Check or un-check the tracks you'd like to have visible in the Track View. There's no need to always see all 100+ tracks in your project. You can select multiple tracks at the same time, and change their visibility status by pushing your computer's space bar.
Once I've bounced, I routinely Mute and then Archive those MIDI and sample player audio tracks, and then also make them invisible via the Track Manager.
As Randy mentioned, I can't over-emphasize the advantage to having logically named tracks ... especially since Sonar uses those track names for various processes. It's really the only way to fly. I also correlate all my MIDI and Audio host tracks with channel and port numbers and so forth ... if I end up with an orphaned track, I can easily see where it belongs.
I'd like to offer another project management tip that has made Sonar DAW life WAY more organized ... Track Folders.
Despite using Sonar 8 (which has those composite "Instrument Tracks"), I still prefer to use separate MIDI and Audio tracks for my various Soft Synth tracks (both VSTi for the Garritan stuff, and ReWire for my Giga handshakes).
My master Track Templates are set-up with MIDI folders for each orchestral section, I.E., Rhythm Section; Reeds; Brass; Strings; Percussion. These folders contain all the MIDI tracks for my virtual pit (or Jazz band, or orchestra).
Each of those MIDI folders then also has a related Audio Folder, I.E., Rhythm Section-Hosts; Reeds-Hosts; Brass-Hosts; Strings-Hosts; Percussion-Hosts. These folders contain all the audio tracks that handshake with the soft-synths ... hence the "host" nomenclature.
In addition to the soft-synth audio host folders, there's also audio-only folders set-up for "Audio-Mixes", "Audio-Vocals" (for live vocals), "Audio-Instrumentals" (for ,say, a live sax part), etc.
The nice thing is that although I usually have over a hundred tracks in my typical project set-up, I can just display the relevant tracks that I'm working on with a single click on the folder header. There's an Open/Close toggle, and when closed, the folder only takes up a single track height ... very "Vertical-Friendly"! . It's also great for soloing or muting an entire section ... there are M-S-R (and now, Archive) buttons on the folder header and all component tracks are affected.
If you have any questions on Sonar folders, feel free to ask! I love 'em! I listed my folder set-up which matches the way I work, but you may see other potential ways of implementing them. I'm going to suggest to Sonar to make them available from the PRV ... that would be awesome!