I'm not sure if this is a setup or what, but I'll bite. First, make sure your receiver is set up properly. If I recall, your AM6's are wired so that you run your speaker cable to them, then out to the sats. Is that correct? If so, set your receiver to "LARGE" mains, "SMALL" for center & surrounds, and "NONE" or "OFF" for the subwoofer. This will route the bass & LFE channel to the fronts/"sub" in the AM6.
You'll find, though, that your bass module is really a "detached woofer," not a true subwoofer. I'd say a sub has to be able to play cleanly down to at least 25 hz or so to truly be called a subwoofer- yours simply can't do that. So whatever inhabits the lowest couple octaves really won't be audible. Moreover, the bass module is probably being overloaded badly by heavy movie bass. I'm not totally clear on whether you mean it gets nasty during big explosions or that it completely cuts out...If the former, you can remedy this by adding another subwoofer, although integration might take some work.
It could also be that your receiver is running out of power & clipping badly during the loud parts. In all likelihood you're looking at both.
I'd guess your rig is probably fairly robust down to 50 hz or so, with probably a bit of a hump there. Below that the output is likely down quite a ways (depending somewhat upon your room- you get a little "room gain" in most instances, but it's variable).
The most common advice you'll probably get here is to ditch your speakers and move up to something a bit better. Audiophools generally develope "upgraditus" as they get deeper into this hobby, and I think you'll find there's a lot better out there than the brand you're using.
If you can swing $500 or so, you can get a really killer sub from Outlaw Audio or Hsu Research. A very little more will get you a SVS sub with a built in amp. Compared to what you're getting now, you'll be stunned speechless.