for a 60gal cube you would get a pretty big wave with just one pump. If you are making a really large wave, the pump will have a large effect on your DSB, but only testing will tell how large.
Alternatively you could turn the pulsing down a bit, so that you don't generate a wave. I have an MP40w pulsing on my 30gal cube with a DSB and have no problems.
-Tim