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I am trying to synchronise the differential data acquisition NIDAQmx of a PCI 6031E board (2 channels AI0 and AI8) with an ASIC delivering two outputs (e.g. 3.54volts and 3.53 volts). 


I want to read the difference between those 2 outputs from the ASIC in the NICARD.


First I am trying to find out what my connections should be like regarding AIGND, DGND and the GND of my circuit ASIC:


I am using HARDWARE timing acquisition on NIDAQmx and an ATMEGA128 to deliver a CLOCK to the NICARD and deliver a waveform to the ASIC which makes it send me the data to the NICARD on every CLOCK high.


I attach two sketches of the system IDEA and system connections.