What is your project? Considering that Aquaria's engine is open source, I think they'd let you incorporate the editor into your project, as long as you don't use any of Aquaria's data files. And that you might need to make your engine open source as well, though I'm not sure what the terms of the GPL are (even after reading it quite a few times).
I'd suggest that you don't use the Aquaria editor as-is, because it's still sort of rough. If you can improve it somehow, feel free to do so and contribute the code back to the project.