I am sort of in the same boat as you, but worse off. I am still new to the HT game, so I purchased speakers and a sub that just doesn't "blend" well, this is obviously not your case! I have ity-bity satellite speakers with a HUGE SVS box sub.
I think the "punchy" bass is close to the upper end of my sub's frequency response, or in my case, way out of the range of my mains response. I say that because at work we use JBL control 5 monitors, and they are just a little bigger than bookshelves but they do have punch, with no sub. I do not have "punch" at the house for sure.
In my limited knowledge, I would concur with what has already been said, with the additional possiblities:
Are you used to an exaggerated mid/upper bass response? I am....err was. I didn't wan't "BOOM! BOOM!" when I bought my sub, but I did expect a little more "boom" than I was *initially* getting (read below) from my sub; was kind of shocked. HOWEVER, the quality from my sub is TOP NOTCH, so it stays! I actually enjoy the quality sound from it more now than I do with an exaggerated "boomy" sub.
As was already suggested, try different cross over frequencies, and set your mains to "small". Producing bass from both your mains AND your sub is gonna cause all kinds of headaches; let each one do their intended job and you will be much better off. As far as what cross-over setting to use, although 80 seems to be the norm, I would say that depends on your ears. If you like the quality of the mid-bass better from your mains than your sub, cross lower; if you like the quality of the mid-bass from your sub more than your mains, cross higher.
Finally, EQ. <----- In my case (YMMV) this was the one thing that gave me the most dramatic improvement in overall sound. All the speaker toeing and such of course made subtle changes, but I'm a "casual" listener, not a "critical" listener, but the EQ had the most dramatic effect in my case.
Lastly, pay attention to your sub's "phase" control. Although we think about the cross-over as a brick wall filter, it isn't. Its possible that the phase is incorrect, causing a "hole" at the cross-over frequency, which happens to be right in that area of the "punchy" feel.
I hope this helps...
-Alan
-EDIT- When I did a response graph from the sub, I found I had LOTS of room gain down low, exaggerating the 20-30Hz range. So like you, when I cranked the gain up on my sub, instead of getting more punch, I was getting more bloat, because it was just turning that really low end up even more (too much). Taming those peaks allowed the upper bass to come alive which elieviating that bloat.
