The stock computers have very little adjustability, you have to go aftermarket for more adjustments. But gaining significant increases in power or performance require modifications to the car like exhaust, cams etc. An aftermarket computer/piggy back won't give you a very significant gain on its own. I assume when you say "run better" you mean performance wise.
Aftermarket computers for tuning are best utilised when you have extensive modifications like changing bigger injectors to say suit your turbo or supercharging application or bigger camshafts, ported heads.
If its just a simple filter and exhaust change it doesn't really justify spending big bucks on an aftermarket computer for not so significant gains.