You can have one channel (or even a channel expander on the retract/brake channel or something like that) that opens the chute.

You can have a seperate small servo tied to the flap channel. It is set up such that if the chute opens with the flaps up the chute flies right off the plane (in other words this small servo provides the chute mounting point). If the chute opens with the flaps down, the chute stays on until you retract the flaps on the ground and then the chute releases.