Hello Jeramy,
Because thermocouples produce such small signals (mV range), it is best to apply some sort of signal conditioning before measuring the signal. Gain should be applied to amplify the signal and make better use of the range of the ADC. Hardware filtering helps remove noise from the signal. Please see the following tutorial for more information on thermocouples:
http://zone.ni.com/devzone/conceptd.nsf/webmain/806355D26B7378B1862567EE0003A842
National Instruments offers a variety of signal conditioning products. Please see the following Knowledge Base for information on these products as well as the pros and cons of each:
http://digital.ni.com/public.nsf/websearch/F0196F5B6CD8F60286256D4B00728B78?OpenDocument
To correct the offset, I would run a self-calibration on the DAQ device. You could also reduce the noise in your measurements by oversampling and averaging the signal. That way you don't have to buy new hardware.
Let me know if this does not help.
Regards,
Sean C.