Most likely whatever hardware you are using is setting a single gain setting for all three of your channels. This will be detrimental to your millivolts readings.
Check your gain settings in Measurement and Automation Explorer. You can set a gain for individual channels on some SCXI systems, or many of the DAQ boards allow you to set gain on a per channel basis. In code, you can set the channel's input limits in AI Config to affect gain. Also notice that you can specify a different set of input limits for each channel in the Channel input array.
The example VI's are meant to give you a starting place, but you will need to modify them to customize them for your own needs.
Processing the channels separately is just a matter of indexing the 2D data array to extr
act the individual channels.
If you are unfamiliar with LabVIEW, you should consider brushing up your skills with one of the self-paced course manuals or a customer education class. I know the LabVIEW Basics classes cover how to do exactly what you are wanting. Course kits also come with disks with solutions to the exercises presented. http://www.ni.com/custed