In the case of the PadKontrol and many other controllers, we can send notes on any MIDI channel we want. When we set up a controller to send notes on MIDI channel 1, it doesn't tell FL Studio that it's being operated on channel 1, each note message just happens to be on channel 1. The MIDI channel is part of the note on and note off messages sent by the controller.

So, when 16 channels in FL Studio are selected, the first channel responds to MIDI notes sent on MIDI channel 1, the second on channel 2 and so on. When multiple channels in the step sequencer are selected, the MIDI channel that each note is sent on determines which channel (each instrument in FL Studio, like the 3xOSC and FPC, is called a 'channel', it's confusing) it controls, from the ones that are selected. Now we can configure the MIDI controllers and the channels in FL Studio so that each channel is controlled by a seperate controller.