Arduino Due ADC sampling
As far as I understand, this uC has single ADC harware with multiple channels (multiplexed inputs). This means that, for each conversion, it needs some acquisition time to charge its internal sample-and-hold capacitor and then some time to do actual conversion.
So, the ideal 1 M samples/second is for single channel only. If you use 4 channels, you can have 250 k samples/second max.
Sampling time is also specified for each channel. This device can't sample all the channels at the same time, it must sample them one by one.