Hi, I suggest talking it over with your dealer or with Richard himself.
Sometimes physically moving the sub a few inches one way or the other can have a dramatic impact on bass performance. That is what I'd try first. Moving it closer or farther from the satellites will also affect the phase relationships, and too, the overall bass performance.
Also, if your only choices for phase adjustment are reversed and not reversed, that may not be adequate. Many active crossovers give you a continuously variable phase adjustment, which makes it a lot easier to achieve good results. That's one thing I like about the Paradigm X-30 that I use. It's very effective and simple to dial in.
If your only choices for phase adjustment are reversed and not reversed, then there are only a few positions in your room where you could locate the sub and the phase relationship to the satellites would be correct. One position is with the subwoofer's driver in the same plane as the satellites (probably not the best position for achieving deep bass because most satellites like to be located out in the room away from bass-reinforcing boundaries). The other location may not be where you want it to be, but you could set up the sub for maximum linear bass boost and then reposition the satellites where they blend the best (probably not where they're currently located). Or, you could save yourself a lot of trial and error by using a crossover with the aforementioned variable phase control.
I went through this whole process a few months back when I moved my gear into a new room, so I know what it's like, and I feel for you. Sometimes you have to settle on the best compromise. But with a little experimenting and patience, I bet you can improve the performance.
When I set up my stereo pair of 2Wq's (with my Vandy 3A Sig's), I tried them both in-phase and reversed-phase, and the outcome was similar to what you describe. I subsequently got the Rives Audio test CD (which has test bands that are corrected to work with the Radio Shack SPL meter), and tested the subs' frequency response while making small placement adjustments (as Plato describes). After several hours of moving the subs a few inches nearer or further away from the side and rear walls, and driving the subs in-phase, I eventually got a much flatter frequency response. The Vandy subs, in my experience, take a good deal of experimenting to find the best placement, but then reward you with full, fairly flat response.
The frequency response of the Vandy 2Wq sub also depends on the "Q" setting that you choose. The maximum "Q" setting (lowest number on the dial) gives you the flattest response, while the higher settings have a pronounced "hump" in the frequency response. When adjusting your sub(s) your subs, I advise you to begin with them in-phase and the "Q" setting at its lowest number.