Data Acquisition Idea Exchange

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:

http://zone.ni.com/devzone/cda/tut/p/id/3344

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.

Thanks.

Javi.