Any DAQ card you choose will (as a rule) only use 1 input channel (channel 0) for data transfer between the SCXI chassis and the DAQ card. All of the data is multiplexed through channel 0 of the onboard DAQ card. So, you only NEED 1 analog input channel on your DAQ card. The 6011E is not the best choice for SCXI since you can not use the inherent (pseudo) SSH capability. In addition, the SCXI bus is band limited to a maximum aggregate sampling rate of 333 ksamples per second. So, the DAQ board would be limited to the 333 ks limit with SCXI. My personal favorite is the PCI (or PXI) 6052E board. It is rated at 333 ksamples per second at 16-bit accuracy - it is a superb match with the SCXI line.
As for the question about single-ended or differential
, well.., that is an entire DAQ lesson in itself. Simply put ... Single-ended means you connect the positive inputs to the designated channel and all of the ground are tied together. Differential means you attach the positive and ground inputs from each sensor to individual channels (see the appropriate users manual). Differential gives superior signal-to-noise ratio and commom mode noise rejection - at the expense of twice the channel count. The "gross rule-of-thumb" is: If your signal source is grounded (by means of a three-prong plug - say a stand-alone Vischay Amplifier) and the signal is greater than 1 V, and, the input wire is shielded and properly grounded, and, the wire length is less than 10 feet -- you can use single-ended: Otherwise, use differential.