Currently there is no way to accomplish this. The Growl mailing lists have discussed allowing Growl to always place the notification on the display that you have a window focused in.
For example, you have 3 displays, oriented in a horizontal line, and you're doing some file management on the far-left display and web browsing on the far right. If Finder has focus, the notification will be shown on the far-left display, if Safari/Chrome/Firefox/$BROWSER has focus, the notification will be shown on the far-right display.
But this feature has not yet been implemented, so you are limited to explicitly configuring Growl to send notifications to a single display.
This feature has been written up on their Google Code Project page, so you can star the issue in order to receive further notifications.
Note that you can star it on an issue detail page by clicking the star outline to the left of the title "Issue 122: [...]", or at the bottom of the page just above the comment box. After clicking the star in either location, it will turn yellow and have a thicker blue outline, that means you've subscribed, and in essence, "voted" for the feature.
OSX has to guess which monitor is which, since the EDID info is the same for both (save the serial number, presumably, but OSX doesn't appear to pay attention to that). It usually tries to set things up to the previous setup by looking at how the devices are attached in the connection tree, however with Thunderbolt the connection tree isn't as simple as it was with displayport and USB.
You should be able resolve this by attaching one monitor at a time (ie, unplug the thunderbolt connection for the third monitor, attachthe second, then plug the third back in). However that's less than ideal, especially since all your apps will go back to the main monitor, rather than how you had them set up previously.
When Apple releases a refresh of the thunderbolt display, attaching one of the old ones and one of the new ones should also resolve the problem - they won't appear to be the "same" device, and so OSX will have an easier time keeping track of which is which.
Until that happens, another thing you can try is attaching the third one with a thunderbolt extension cable. It's an active device, and may alter the connection tree enough that OSX will have an easier time keeping track of it.
If that doesn't help, your best bet will be to wait until they refresh the thunderbolt display and upgrade only one of them when they do.
Best Answer
You basically need to have your macbook output to two displays, which it won't do easily/willingly.
There are a couple hacks...either doing the display output over USB or using a matrox display. See more info: here
One really hacky solution might be to output via air display to and iPad (hooked up to a projector)for the 2nd monitor. I'll buy you a beer if you make that work. :-)