When you have two sound sources spaced 1/2λ apart, a notch in response appears. It also presents itself at multiples of this frequency. What is happening is dual slit diffraction, and interference patterns form in the listening area. Diffraction effects are present when there is more than one point source separated by distances of this scale. Some places in the room have deep notches in output at certain frequencies.

There are several ways to deal with this issue:

1. Reduce the number of point sources
2. Reduce distance between point sources
3. Reduce maximum frequency emitted by point sources
4. Reduce overlapping frequency bands of point sources
5. Reduce overlapping coverage of point sources using directional control

OK. But that is somewhat academic. So what to do about it?

If you want to use dual woofers as mains rather than subs, I would suggest running them as a 2.5-way speaker, basically crossing over one woofer much deeper so it doesn't share the midrange band with the second woofer. Both woofers work together in the deepest bass frequencies but only one covers the midrange band. The natural orientation is to run them vertically, with a large coil on the lower woofer to attenuate output above 100Hz. The upper woofer serves as a midwoofer, and is used through the midrange. Crossover the midwoofer to the tweeter using the four π crossover.