If I understand your application correctly, your microprocessor is generating an analog voltage, and you are wanting to measure it using a 6229.
In order to do this, you could connect the positive terminal of the microprocessor's output to pin 68 (AI 0) on the 6229, and the negative terminal of the microprocessor to pin 34 on the 6229 (AI 8). You would then want to perform a differential measurement using the analog input functionality of the 6229.
Is there any particular development environment you are using to perform the data acquisition on your PC? If you are using LabView, "Cont Acq&Graph Voltage-Int Clk" would get you started quickly. I wish you the best of luck.