Well, had a go at re-tuning the sub using test tracks. Amasing results!
I played sets of low frequencies on repeat and tried different settings for volume and cut off on the sub, while listening and watching the response on the ipod spectrum analyser. On some tracks I could clearly hear (and see - which basically made me understand what it is) the harmonics, i.e. the additional peaks that should not be there. I could not get rid of them completely but with lowering the cut-off setting on the sub I could see them almost disappearing. So I did this throughout the sub range and ended up with the cut-off setting about a quarter lower than before (was at about 50%, now at 75%, i.e. the sub kicks in lower).
I then played the test tracks again now changing the gain level on the sub (rasing it - as the volume became lower through the previous step). I also played some familiar music tracks with low bass for that. I ended up with level set at about 75% (was at 50%).
The result I could clearly see on the ipod is much reduced harmionics (almost no extra peak at 60Hz when playing 30Hz tone etc). The sub now goes to 25Hz.
The result I can clearly hear is that the depth is better, and the bass became faster, cleaner and kind of airy. The mids and highs came forward as well!
I remember from some sub setting-up guide that this is a common mistake - setting the cut-off too high and level too low. That is exactly what I had. And I thought I was subtle with my sub settings.
So, very happy with the results. I recommend everybody with subs try this.
You do not get a completely flat response of cause (a more advanced bass mgt is clearly needed for that) but the result is very very good.
Next step - trying different sub positions in the room.
And hopefully trying the new speakers in abt 2-3 weeks.