Communication between UIAutomation and the application

Is there a way for the UIAutomation script to communicate with the running application and just send its information, run a function, or change a variable - directly and not through an interface?

I ask because I only use using a script to take screenshots, and it would be very convenient if I could tell the application to set a couple of integers rather than deal with the somewhat unreliable and complex multitouch gesture and timing settings.