Hi, Jon. It's possible to get submicrovolt measurements with the M-series boards, but it's not that easy. Your nanovoltmeter has a bandwidth of probably a few Hz. The 6254 has a bandwidth of around 3MHz according to the specs. Unlike a DMM or nanovoltmeter, the bandwidth of a multifunction DAQ card doesn't drop as the sample rate is reduced. In order to get low noise you need to sample at a high rate and then average or otherwise digitally filter the data to bring the noise down.
On its smallest input range, I see from the specs that the 625x boards have input noise of 15uV rms. It sounds like that's about 100 times higher than you'd like. So you'll need to average 100^2 = 10,000 samples per reading to get the noise down to 150nV rms. That's best case. But there's also the issue of low-frequency noise and drift, which can't be addressed by averaging. DMMs and nanovoltmeters use autozero to get rid of low-frequency noise; you'll have to implement that in your code. You can periodically switch to internal ground and subtract those measurements from your signal measurements, or even better, hook up your signal in reverse to another channel and subtract the readings from that channel. I'm being kind of hand-wavy here, but it can be made to work, if....
Even after you do all the above, there's still the possibility that you'll have noise due to aliasing. Say you're sampling at 1MS/s, and you average 10,000 samples per reading, with autozero thrown in there. That ought to limit you bandwidth to around 100Hz, but any noise within 100Hz of 1MHz will also show up in your measurements, because it will alias with your sample rate. So you may need some analog filtering before you digitize. If you stay with the 6254, you'll have to do that yourself, possibly in the terminal block. The 6284 would probably have been a better choice for you, since it has an internal filter that can be enabled for this sort of application.
So I would say that "he who purchased it" was being a bit generous saying the 6254 could do nanovolt measurements. Maybe you should make him write the software.
Chris