I'm not sure what examples you are currently using, but you might want to take a look at some of the C# examples I've attached. They are all analong input examples and can be easily configured to acquire from more than one channel. Simply change the channel string to 'Dev1/ai0:1', that will acquire data from channel 0 and channel 1. Also, you could use this syntax: 'Dev1/ai0, Dev1/ai1'. I hope this helps!
-Alan A.