Ok first off your talking about two different sets of speakers and different frequencies. (I'm not trying to be a dick here)
What gain are you talking about?? The gain on the amp?? And just my $.02 bass knobs are trash. To me they are used for a poorly tuned system. You should be able to set the gains once for a particular type of music and never really mess with it at all. With my system I can play anything from serious bass music to Kenny G to Korn and it all sounds pretty damn good.
While that's a valid point, it's not entirely true. If you listen to only store purchased CD's, well, that's great. However, if you're listening to a burnt CD, your volume is going to be very different than a properly mastered CD. Also, if you plug in your IPOD, most head units convert the signal to play 3-6 db's louder than a regular CD.
I agree that the bass knobs that come with most amplifiers are trash because they turn down all the levels of the amp. As you pointed out, this can cause clipping issues at high volume and generally poor sound quality. I prefer a line level adjustment knob which is a very clean version of a "bass knob," it turns down the input to the amp, this way I can listen to whatever someone has at any particular time.
Whatever way you decide to go though, filli57, Hannibal is correct on his tuning methods and Bob is correct in his last post.