If this is your first two stager, I'd recommend firing your sep charge about one second after burnout, and your motor another second after that. Velocity is your friend, and so is altitude. You absolutely need some kind of sustainer ignition lockout, a direct tilt-detect is best but baro velocity works well too (as long as you're under 800 fps), as does baro altitude. Sim the crap out of the flight, with different motors, so you pretty much know what to expect in terms of altitude and velocity at the time of sustainer ignition and a few seconds afterwards (since you have to take motor pressure-up time into consideration).
Even then, doo-doo happens... I launched a two-stager yesterday, and the J800 in the booster blew through the forward closure, resulting in a RUD at about 300'. Because of the tilt lockout in the Proton, the sustainer did not fire, and all of the parachutes came out since "apogee" had been reached (although the torching in the booster actually melted the Kevlar shock cord). This is an example of a "successful failure"... when it doesn't do what you wanted it to do, but it does exactly what it was programmed to do in the event of an anomaly and therefore everything comes out OK.
