I use Battery 3 for my default drum synth, but the principles should apply to any drum synth.
What I did was to create several custom kits, where I started with whatever particular kit sounds worked for the given project. So, I would open whatever kit was going to be my base kit for the project, but I would choose the Battery 3 version with all of the available outputs - 32 of them.
Then, for each drum cell I was planning to use, I set the output channels so that each drum cell output to a different output channel. I then saved the kit with an indication that it had multiple outs in the naming of it.
Them in Sonar, I created a special project template where I created a Track Folder for Drums, and within that track folder I had a single midi track for all drum midi data, and then inserted a bunch of audio tracks, one for each drum cell from the custom kit I had created.
After naming each of the audio tracks for the corresponding drum kit cell, I saved the project as a template, so that I could start new projects for this particular drum kit and have all of the above all preset for instant access to all of the settings and track-routing. I also did some basic level settings for the kit as a whole prior to creating the project template.
Using the above approach, I capture all midi data in one track, which can still be easily edited, and then I have each drum/cymbal routed to its own audio track. This gives me complete control over each and every kit piece, for effects and levels, and I have no issues in editing the midi data either.
Please note that Cakewalk intends that you should NOT use a drum map to create midi clips using the Step Sequencer. If you try to do it, you will have many problems trying to go back and do editing, so just do not se drum maps with Step Sequencer. I created a little mapping of my custom drum kits that lists the note numbers for each of the kit pieces, and that makes data entry and editing easy - I just look up the proper note number for whatever drums a particular midi clip wll use.
Bob Bone