Space Question

This one goes out to the Space Shot lovers out there (Yes, krjalk, I am looking at you)

So I have been looking at rockets again, specifically multithruster rockets similar to what Armadillo are eventually aiming to build. Now the Soviets played around with these and had no end of problems, most commonly that variences between thrusters couldn't be countered fast enough and the stack tended to fall over. (There was also some pogoing, but I wonder if it was related)

Now the way I have been thinking about it, we're basically balancing a long thin construction on a relatively small vector. It's like balancing a pencil on the tip of your finger. It is inherently unstable so you are having to continuously "tweak" your engine output.

Now what stops you mounting some Peroxide thrusters higher up your stack and rather than trying to balance everything from below, you do your "quick" adjusts from the top of the stack, which means your primary rockets don't need to be anywhere as sensitive in terms of response time?

I am sure there is something I'm missing (The obvious one is that you are putting stresses across the entire stack frame that may make your stack snap in two) but what?