The VI that sets up the DAQmx task does not update automatically; it's generated once, at the time that you convert from the express VI. You can modify it yourself to add extra channels. However, if you're configuring your tasks in Measurement and Automation Explorer, you can remove the DAQmx setup VI and replace it with a DAQmx Task Name constant. Place the task constant on the block diagram and select the task you configured in MAX. One disadvantage to doing this is that your VI is less portable - if you copy your VI to another computer you need to copy the DAQmx configuration too.
About the array transposing - that's partially my fault for providing quickly-written sample code without checking it carefully. The for loop should iterate once for each channel, but you have a different number of channels in each task, and the for loop will only loop as many times as there are rows in the smaller array, so some data from the larger array won't get processed. Separate the Mean functions into two for loops, one for each array, and you'll get more reasonable data.
