Hmm, possibly... First off, I'm assuming you want it to reach orbit. However, even if you don't, MechJeb's autostaging is a persnickety little feature that is, oddly, independent of the Ascent Guidance module. In the Auto-staging section, you can see that I have put a 6 in the Pre section. Basically, what should happen is that if you run this, assuming stage 2 and stage 3 are just lighting engines, without any decouplers, then MechJeb will automatically activate them because that's the way it does things. Then, if the next staging event is a decoupler that gets rid of the first thing, then MechJeb will discard it when it runs out of fuel, however, unless you are quick and change the value here mid-flight, it will discard it 6 seconds after it runs out of fuel. Probably what you want is to set a 6 second post-delay, which is a period of time after activating a staging event that MechJeb will wait before it activates the next stage. In short, Yes, play around with the numbers in the auto-stage section and you will probably find what you are looking for.