All of the channels on a NI-4472 have to be sampled at the same rate because there is only one clock source. This is typical on most acquisition devices. It sounds like you are only using two channels, is that correct? If so, I would recommend running both channels at 20kHz since there is not a data throughput bottleneck. If you truly need for one channel to be sampled at 1kHz, you can always decimate the data in software. You could just use every 20th sample and throw away the rest or you could average every 20 samples together. These are just two ways that you might choose to perform data reduction.
-Jack