Adam,
I was using only Audyssey for a bit, and then added the 1124. The proper way to use it is to use REW and take room measurements so that you add room specific filters. However, Tom Danley issued some recommended filters based on inherent peaks in the cabinet when measured outdoors. I employed these 5 filters, and it made a marked improvement in mine. It's not a subtle tweak. In a nutshell, the cabinet has nearly a 20db peak in it at around 54hz. Therefore, when you set the channel level using pink noise (or the receiver sets the channel level) it is a skewed measurement. The filters knock those peaks down and when the receiver remeasures the channel level, it should be roughly 10-15db higher. Essentially, the lowest octives of the sub are able to now make more impact.
I also read that if Audyssey is employed after the sub EQ that it is able to do a better job because it's not dealing with such large peaks.
Sorry if you knew all that, but that's the simple understanding I have.
There are many other EQ options that are more desirable to most folks, but I got the 1124 off ebay for $30. I don't feel a need at this time for anything better.
The 1124 is confusing to program, but if you get one, PM me and I can help you through it.