Success!!!
Okay this got a bit complicated, but I found the right mix of software to make this work. So here's again the hardware and software setup:
TD = Thunderbolt Display
CH = Channel
MBP = MacBookPro
L = Left Speaker
R = Right Speaker
TD1 (L/R) | TD2 (L/R) | MBP (L/R)
iTunes => SoundFlower => Jack => Aggregate Device => 6 speakers!
Stereo audio only has 2 channels (left and right). So the trick is to get 2 system channels to map to the 6 speaker channels I have.
Step 1: Setup an Aggregate device to merge the 3 sets of speakers into one aggregate.
1-1: In Lion, go to Apps > Utilities > Audio MIDI Setup
1-2: Click the + in the bottom left and select Create aggregate device.
1-3: Select the 3 devices: Built-in Output, Display Audio, Display Audio (there are 2)
1-4: Click Configure Speakers
1-5: Select all 3 streams at the top
1-6: Click Multichannel and then select Hexagonal (this gives you 6 virtual speakers in the graphic)
1-7: I don't think this step is required, but map the channels to the right locations. For me this was a little confusing because TD1 was channels 3 & 4, TD2 was 5 & 6 and, and MBP is 1 & 2. From top left going clockwise, I selected 4, 5, 1, 2, 6, 3.
1-8: You can click the speaker for each one to hear a test tone to make sure you have them right. It's right if the 2 left ones come out of the left screen, the 2 center ones from the center screen, and the 2 right ones from the macbook.
1-9: Right down the numbers so that you know which ones you want for left and which ones you want for right.
Okay, now this is enough to get audio from 2 devices, but stopping here you'd lose your volume control and 4 of your 6 speakers.
Step 2: Install 3 apps (all free):
2-1: Download SoundFlower from http://cycling74.com/soundflower-landing-page/
2-2: Download JackOSX from http://www.jackosx.com/
2-3: Download JackOsX Autostart from http://www.jackosx.com/
Step 3: Setup Jack
3-1: Install Jack
3-2: Start JackPilot and go to Preferences
3-3: Setup input-output device as Aggregate Device that you setup in step 1
3-4: Interface Output Channels should show 6 (6 speakers!). Set Virtual Output channels to 2 (stereo)
3-5: Uncheck auto-connect with physical ports
3-6: Save changes and start the Jack server if it's not running.
Step 4: Setup Soundflower
4-1: Install Soundflower
4-2: Click the flower in the task bar and then choose JackRouter under the 2-channel at the top
4-3: In Lion, go to Apps > Utilities > Audio MIDI Setup
4-4: Find Soundflower (2 ch) and click it, then on the right select Output and then configure speakers
4-5: Select Stero and then set the left speaker as 1 and the right as 2. Testing the speakers here will likely do nothing. That's okay.
Step 5: Finish Jack
5-1: Go to Connection Manager
5-2: Note: this part was a pain -- the UI is funky, so be patient. Click only how described.
5-3: Open the various sub-sections until you can see Soundflowerbed under the Send Ports and see out1 and out2 (the stereo ports) and the System under Receive Ports and you should see playback_1 thru playback_6
5-4: Carefully single-click out1 then double-click the first left speaker channel. Single-click out1 again and then double-click 2nd left speaker channel. Single-click out1 again and then double-click 3rd left speaker channel.
5-5: Carefully single-click out2 then double-click the first right speaker channel. Single-click out2 again and then double-click 2nd right speaker channel. Single-click out2 again and then double-click 3rd right speaker channel.
5-6: Close the connections manager
Load up iTunes or something else and play music. If everything is setup correctly, all 6 speakers should be going with 3 left playing the left channel and the 3 right playing the right channel!
And since you're using Soundflower, your volume controls on your keyboard, etc, should work just fine. Note: you can tweak your individual volume controls back in the aggregate device setup if you need to fine-tune something.
Hopefully that all worked for you! Let me know how you made out!