1. Put the robot under PID control, (i.e. set k_effort[0:28] to 255 for all joints), then
2. Get the robot back on to its feet with your own controller. Drive Atlas into PID controlled Stand pose (for example, see VRCPlugin::SetPIDStand() for approximate target joint positions taken from a snapshot of joint states while standing).
3. Once the robot stabilizes, you can then switch to BDI STAND mode mode and set all k_effort[0:28] to 0 simultaneously (for example, see SetBDIStand() for reference).