I would route input into one of the Arduino’s unused digital pins. Simpler and more straightforward to use in your control logic. You can read the Gpio state out of the HamShield, but the library doesn’t have a function for reading a specific pin at the moment. I could pull up the spec and let you know the details if you really need the HamShield to be the input, but I don’t have it on me at the moment.
As far as DTMF decoding, see my pull request on GitHub. The currently released library doesn’t work as is. My PR fixes it and the comments explain basic use (as follows from the SoC programming guide). With my library changes I have successfully decoded tones from my HT. Note that you do also need to route the squelch state pin into a digital pin on the arduino to make effective use. The dtmf support in the chip runs continuously when enabled independent of SQ. So it’ll detect codes in the random noise.