The Sonar Patch Change event is based on the MIDI Patch Change. In the 1980s when MIDI was developed, synthesizers had a few dozen patches, and there was no concept of higher level groupings like Combi and Performance.
 
I would like to be able to explicitly save specific Combi or Program settings on MIDI tracks in Sonar.  A Patch change at the beginning of the track can only set within the current mode - whether it is Program or Combi.  As far as I can tell, only a SysEx message can change between Combi and Program mode.
 
Another problem is with the INS files. The INS file has no concept of the distinction between Program and Combi modes.  The same MIDI patch change messages are used to select Program Int-A000 and Combi Int-A000.   But programs and combis have different names. If the INS file is created with the program names, the names will be wrong when selecting a Combi.
 
One possibility would be to generate different INS files for both the Program and Combi mode, but the only way of mapping them is by MIDI channel. Putting Programs and Combis on different MIDI channels is undesirable because it interferes with the "normal" use of MIDI channels.
 
Has anyone developed any work-around or technique to make it easier to work with modern synthesizers that have both Programs and Combi/Performance, etc?
 
 

I've never heard of 'Combi' or 'Performance' in this context, so I would guess that they're non-standard. If so, a SysEx message is the only way you can access these features from a standard DAW. Perhaps if there are common hardware units that use such systems then it would be possible for a DAW to support that directly, but given that soft synths seem to only use Program changes (eg. Kontakt lets you set up an Instrument Bank of 128 different instruments and switch via program changes), it would seem that there isn't likely to be a lot of demand for this sort of functionality, unfortunately.

Are you talking Hardware Synths?
 
My JV1080 has both modes of either single patches or combination patches, I have it set by default to turn on in single voice mode.
 
If I am using it in Combi mode I embed a Sysex message in the Project to set it in combi mode.  Then select the required combi patch on channel 16, using bank select and patch select, as is the way it works.
Then use separate midi channels to talk to the different voices within the patch.
 
Is there something else you require, it does mean a little work in the Instrument definitions section of Preferences but once set up.  Once set up backup the Master ins file so it can be made portable.

The terms I am familiar with are Patch mode and Performance mode. I have an XV 5080. I have always looked at Performance mode for MIDI triggering use and Patch mode for live triggering. Both are triggered by MIDI but the Performance mode allows all 16 channels to be used. Patch mode is for using the entire synth for a single sound.  Layering various patches on top of one another.  Performance mode is used to have each channel play a different patch. The only reason this is the way it is is due to the limitation in total memory a hardware synth has. The number of voices is also limited. 
 
To my knowledge the way to trigger patch mode and set up a patch is via sysex. With performance mode one can use normal means to control patch changes and use an instrument definition.   

Yeah, you're going to have to elaborate what you're trying to accomplish. I set up my Yamaha EX5R with an instrument definitions including bank select messages. I set the synth up with some commonly used instrument groupings and a "Blank Sonar " patch when I wanted to build it on the fly. There is a knowledge base article on bank changing and instrument definitions you can google. On EX5R single sounds are Voices and multi timbral groups are Performances.It has instructions for MSB and LSB number calculations. It's some work, but once you're done you have it forever.

To elaborate, I want a project to set my Kronos to the proper patch (whether it is program or combi) when the project loads and/or starts playing.
 
The "traditional" model is that every MIDI track in the project corresponds to a different MIDI channel, and you send program changes and MIDI data on those channels to the multi-timbral synth. This still works fine with software synths, but things are more complicated with modern hardware synths that have additional functionality at the Combi or Performance level.
 
Using the Kronos as an example, the Combi often contains specific Karma (arpeggiator and automation effects) and specific insert effects routings.  Even though a combi is based on a number of "timbres" that may be on different MIDI channels, there may be more than one timbre assigned to a a single MIDI channel. So the behavior of a Combi cannot be duplicated by just emitting program changes on several MIDI channels.
 
For those reasons, I have a number of projects that are based on a Kronos Combi, not discrete programs.
Thus, there is a need for Sonar to put the Kronos into Combi mode, and select a specific Combi, to properly initialize the instrument for the Sonar Project.
 
With the existing INS file, there is no concept of a "Combi".  The best I can do is hand-edit a sysex message in the Event View to select the Combi mode, and then send a program change to select a specific Combi.  That's just the first issue. In addition, when I edit that Patch Change event to select a Combi, the Sonar instrument definition knows only about Programs.  So if I want the Combi at Int-A005, the Patch Change dialog will be showing me the name of the Program at Int-A005.
 
By the way - for anybody that has a Kronos, I wrote a little utility to convert the Kronos PCG file to a Sonar INS file:
http://www.synthify.com/Kronos_SW_dev/index.html#PCG2INS
 

I vote for the various explanations above using a sysex that is transmitted when the project is opened. To help with the program/combi(performance) change conflict, set your synth to receive combi program changes on a dedicated master channel that is different from your instrument channels. You probably have a limitation of 8 instruments in a combi anyway. Then in your ins files, assign your combi bank patch lists to that channel.
 
P.S. you can probably record the specific mode select sysex messages while operating the synth front panel. Record them into the sysex bank page of your template project.

At some point in the history of Cakewalk and Sonar, there was an ability to specify a MIDI "setup" message to be sent on project load. I thought it was part of Project Info, but I don't find it there now.  Does anyone know where that function has moved?
 

Probably hasn't moved in a long time. It's part of Sysx View.
 
Put your sysex banks into the Sysx View. Highlight one you want to send, then in the Sysx view Settings menu choose Auto Send On. Then configure the midi output port you want to send it to. Do that for multiple banks if you want. One more config option is whether you want Sonar to ask you or not each time you open the project whether to send those banks or not.
 
Covered in "Sending Sysx banks at startup" in the manual.

Would it be possible to create two different instrument definitions for the same piece of hardware?  One that addresses what the OP calls Programs and the other to address the Combi?