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I know with FreeFone, it runs in the background, and when a call comes in, it pops up the caller screen. I am not sure what is triggering that, but you should be able to tap into that for incoming calls.
As for calling out, you can put code on your Dial button to switch the audio. You could also put code on the hang-up button to mute the line in.
I wish I knew more specifics, but see no one else had a response, so this may help guide you in the right direction
If all else fails, post a message in the freefone thread, and maybe CDRSkull can tell you of any hooks into it.