What you are probably hearing is bass in the 60-100 hz vicinity (typical for dance/pop/rap/rock). If you tried to play actual subbass, a 6x9 will not be able to produce it with any substantial levels. I think you are probably mistaking boom with bass that is on the source material. The other thing that happens is that it is not uncommon to mis-tune a ported enclosure which results in a boomy system. A good quality subwoofer installation with good components properly installed will sound noticeably better, clearer, louder, punchier (or whatever other adjectives you want to use) than a system relying on 6x9 to provide bass.
By the way, if you were to here a perfectly flat system response, the bass will be pretty weak sounding to most people.
