Martin,
The sentence on dithering is not worded as well as it should be. You only want to average a DC signal or a very slow AC signal. Consider sampling an AC signal at 1 MSPS and averaging 100 pts. That is effectively 10 KSPS, so according to Nyquist, that's a 5 kHz signal. If you want a decent representation of the wave (10 Pts/cycle), the frequency is effectively 500 Hz. Thus, high speed signals and averaging really don't make sence being talked about together.
You can only turn dithering on or off for the entire board, and yes it would be best to enable dithering on both card.
Nick Wilson
National Intruments
www.ni.com/ask