Hi,
Because it just measures the potetial difference between the 2 pins it does not really matter. i would stick with the +ve going to the first channel of the pairing and then the -ve going to the second. You then have to go into Measurement & Automation explorer and create a virtual channel. In here you right click data neighbourhood and create channel....go through the steps, I.E analog input, device type, input type as just a voltage....and then on one of the later screens it tells you the exact pins to connect the wires to and gives you the option to select RSE NRSE or differential input type....as you change the connection type the pins guidance changes accordingly. its quite straight fwd and very easy to follow using this wizard.
Cheers
Lee