Let me explain. Your board has a single A/D. There is a mux that rapidly switches between channels. It will take a sample from channel 0, then channel 1, then channel 2, and then start all over again. It will repeat until the total number of samples that you requested have been taken. The switching is very fast - on the order of usec, so you can take the 3 measurements but it is not truly simultaneous. Depending on the frequency and the accuracy of the phase difference you're looking for, this may not make a difference. You can also get the inter-channel delay and compensate for it.