I was encouraged by Arthur Kay to start a thread here after I posted some frustration on Twitter, so here we go.

First off, the instructions for setting up the Packager were great and I had it installed and ready for usage in a couple minutes.

Second, I specifically scoured the documentation to see if there were any special instructions for getting an ExtJS 4.1 project that I'm building with Sencha Command to get packaged. I didn't find anything so I assumed that following the basic instructions would work.

That's what I did.

I created a projectConfig.json file in the root folder of my project. The source for the UI is contained in a www sub-folder. I then use Sencha Command to build that project into a sub-sub-folder of www/build/crescendo/testing.

So here's my config file.

Code:
{
       "applicationName": "Synthesys Explorer",
       "applicationIconPaths": [],
       "versionString": "1.0",
       "outputPath": "packaged",
       "webAppPath": "/Users/stevebrownlee/DRProjects/synex-demo/www/build/crescendo/testing",
       "settings": {
           "mainWindow": {
               "autoShow": true
           },
           "remoteDebuggingPort": 9100,
           "security": {
                "allowFileSystemAccess": true
            }
       }
   }
So I then ran ionpackage crescendoConfig.json and it ran fine. Inserting output here for sake of completeness.

Code:
 -- License is valid
Packing from configuration file crescendoConfig.json...
Output path already exists. Overwrite (Y/N)? y 
Output path will be overwritten.
Searching for files. Please wait...
Total of 2315 files to be packaged.
Target package file /Users/stevebrownlee/DRProjects/synex-demo/packaged/app.ion
Package created at /Users/stevebrownlee/DRProjects/synex-demo/packaged
Package /Users/stevebrownlee/DRProjects/synex-demo/packaged/app.ion (28250844 bytes) is verified. Everything looks good.
Encrypting package with basic encryption...
Package encrypted successfully.
Extracting run-time to /Users/stevebrownlee/DRProjects/synex-demo/packaged
Run-time is extracted.


---------------------------------------------------
NOTE: You are currently evaluating Sencha Desktop Packager 1.1.
Your evaluation period will end in 29 days.




Applications packaged using this evaluation edition will function
for 14 days from the date it was packaged.


Visit http://www.sencha.com/contact for more information.
Awesome so far.

However, when I launch the packaged application, I get a blank screen and when I open up Chrome inspector and point it to the debug port, the HTML is there, with links to all my resources and script tags for my scripts, but, alas still a blank screen.

So my assumption that I could simply run Sencha Command to build my project, and then immediately run Desktop Packager against that build directory was a false assumption.

The thing is, I can't glean anything from the documentation that comes with the packager about what I'm doing wrong.