You're more likely to burn up whatever speakers you are powering with the amp due to incorrect settings but in extreme situations it is possible to burn up the amp as well.
yea the only way you could blow the amp by tuning is with the gain setting i believe and just like prowler said you'll probably end up blowing the speakers if the settings are wrong.
Of course it all depends on the amp and speakers in question. It's perfectly possible to toast an amp by setting the gain too high and clipping the output, exceding the duty cycle of the output devices and releasing the magic smoke.