Coptop,
The Y6 is a *complicated* example of this, but we'll go with it . . .
First off, layout orders are dependent on the controller, and if the controller has a raw mixer capability, you can change that order completely, but you're on your own after that -- Most everyone else will be using the default mix for that board's motor layout.
So to pick an order, we'll call 1-6, moving clockwise from front-left to rear, odds on top, evens on bottom. We'll also pick rotor directions for CW - M1,3,6 and CCW M2,4,5.
Why is the tail reversed? Because. In my analysis, it gives very little advantage. I've seen some fancy hand-waving about canceling torques. I don't agree, but doesn't matter -- *EVERY* board layout I've seen flips one pair, either on the tail or right boom, and it doesn't hurt anything. As I mentioned before you can always manually change the mix to flip that pair back, but other headaches you run into may make troubleshooting help . . . complicated. YMMV.
So on to the inputs:
Roll: M1&2 increase with positive roll, M3&4 decrease with positive roll M5&6 maintain
Yaw: M2,4&5 increase with positive yaw, M1,3&6 decrease with positive yaw
Pitch: M5&6 increase with positive pitch, M1,2,3&4 decrease proportionally less with pitch, depending on how far forward they are relative to CG as 5&6 are aft of CG.
In the end, the board manages this for you. Until you're ready to break things in the mixer, it's nice to understand, but best to let this be transparent.
