What is between the speakers? I know that sounds like a strange question, but what I am asking is, is there a TV between them, an AV Equipment stand, a chair, etc....?
You speaker are front ported so that is a plus. But being that close to the wall will re-enforce the bass significantly.
Just curious, how does the system sound without the SUB?
Next, it seems that you have the speakers connected directly to the amp. If you connect them to the Sub, the sub will filter some of the low frequencies from the front speaker. Though, usually there is just a huge capacitor doing that filtering. Most don't consider this the best method. But you could try it and see if it improves things.
As to bi-wiring, if you are using proper sized wire, most don't feel it adds anything. Still, do as you please.
My speakers are place on either side of an equipment/tv stand. The stand is about 6" from the back wall to allow me to get at the cables and wire. To be in-line with the equipment cabinet, the speakers are about 9" to 10" from the back wall. Though even 10" is still considered pretty close.
If you are in a similar situation, you could move the equipment cabinet forward, and then also move the speakers forward to match.
So, here is the first thing I would try.
1.) Try listening to the system without the Sub, and see if it sounds more like you want it too.
2.) Next as an experiment, move the speakers about 12" from the wall, and see if the smooths out the bass. What we are trying to do is isolate the source of the problem.
3.) Next, connect your speaker to the Speaker Output on the back of the Sub. That should filter some of the lows from the main speaker. It is up to you to decide whether you like the overall sound of this. Most are inclined to think the large capacitor, while filtering the bass out, also interferes with the sound quality. I've never tried it so I can't say. But again, we are trying to isolate the cause of the problem.
I suspect it is partly a problem of speaker placement relative to the wall, and the fact that you can't set your amp to 'small'. AV amps have internal electronic filters that keep the low-bass and mid-bass separate. The low bass goes to the Sub, and the mid-bass goes to the front speakers. In a stereo configuration, low-bass goes both to the sub and to the front speakers.
A quick look at the Wharfedale site indicates they still have product brochures and manual for these speakers.
Powercube brochure -
http://www.wharfedale.co.nz/Site/WHARFEDALE/files//powercubes.pdf
Diamond 8 Series manual -
http://www.wharfedale.co.uk/images/ranges/manual_4.pdf
New Powercube Plus manual -
http://www.wharfedale.co.uk/images/ranges/manual_17.pdf
It seems that the Crossover control goes from 70hz to 170hz. I think we can assume it is linear, so 50% turn is going to be about 120hz. A 33% turn is going to be about 100hz. I think in your case, you could set it as low as it will go.
Another options is to try plugging the bass port on the front speakers. This will soften the bass, and cause it to roll-off earlier and slower.
Next, from glancing at the brochure on the sub, it has to very large bass ports on the back, how close are they to the wall, and were is your sub placed in the room? If it is close to the wall, you are probably getting interference with the rear ports. If it is in a corner, you are probably getting a double bass boost from the two nearby walls.
Play with these ideas for a while and see what you discover.
Steve/bluewizard