Yup, I stressed about the receiver wiring too, but the transmitter setup wizard takes care if that, so just plug them in any order you want! However, on my reciever I believe the connector that has all 3 wires must go in channel 1 to power the receiver. The connectors do need to be in the right orientation though (your receiver probably has marked which column of pins is signal, positive, and negative).
The flight mode setting is a way to change 'on the fly' what flight mode the quad is in. To me, that's something for a more experienced pilot who sometimes wants their quad very smooth/stable and other times wants it very responsive/snappy. I didn't bother setting that to a switch or anything at first, I just made sure there was only one flight mode setup in librapilot.
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