Pui -
Thank you for posting on NI's Discussion Forum.
I have good news and bad news. The good news is that it is possible to synchronize digital input and analog inputs. The bad news is that it is not possible with any E-series DAQ device.
Possible solution: Read both analog and digital inputs as analog inputs. You can programmatically evaluate whether the input voltage should be interpreted as high or low. I have done this several times very effectively!
Best of Luck,
Erik