Kent,
The Modulation Toolkit is fairly robust. I believe that it will work fine with the 20 and 200 MS/s boards. However, these obviously have to stay towards the lower frequency end of the spectrum. The Modulation Toolkit is most powerful with NI's RF products and is designed to do so. However, as I said, I believe that since the MT stays mostly on the software side and does not care too much about hardware it will not care about where the signals are coming from and will work for you.