Hm, not sure if this will answer your questrion, but ATD0 and ATD1 are two different instances of ATD module. Each one handles different set of analog input pins (channels). I don't know what MCU you are talking about, but for example on S12XD ATD0 has 8 channels and ATD1 - 16. Depending on package size, some ATD pins may be not bonded out.