Under the old firmware, you only had two choices - all channels digital, or all channels analog. So if you wanted to source some channels from a digital mixer and others from an outboard analog mic pre, under the original firmware you couldn't do it.
The new system is a lot more flexible. You get to choose how each pair of channels is sourced. Channels 1 & 2 can be set to either analog or digital input, same again for channels 3 & 4, and for each pair up through 23 & 24. The control for this option is on the Utility menu - that's where you set how each pair of channels is routed.
The "Input" button on the front panel still lets you choose between all analog and all digital, but now it has a third "mixed" state as well. When a mixed set of inputs is in use, the front panel will light both the "Analog" and the "Digital" indicators at the same time. So the button will toggle through three states: "Digital", "Analog", and "Analog/Digital". When the third state is engaged, the settings in the Utility menu take effect.