The APM wiki shows that I should use only the input wire (white) on all the motors to APM board except for motor 1 which I should have a three wires (white, red and black) plugged in. Is this recommended and what is the reason. Will bad things happen if I plug all three colors in with all 6 of my motors to the APM 2 board? Please explain. Thanks.
The red and blacks wires are +5V and grounds. The APM takes its power from this +5V and all the +5V pins of the APM are connected together. If you connect red and black wires from all ESCs you are shorting the their +5V outputs together (trough the APM connector). This is not good because the +5V of all 6 ESCs are not exactly the same and the one with the higher voltage will end up back driving the other ESCs.
So follow the recommended connections if you want to avoid problems.
I will remove all but one red wire from APM. Should I do the same with the black ground wires? I suspect that the grounds would not matter?
Keep the black ones (ground), so that you know for sure that you have common ground for the control signal (white wires).
Thanks to everyone for your answers.
The additional black wires are not necessary but they do not do anything wrong so you can keep them
Umm... Where do you think that signal wire voltage will go if you cut the black wires?
All ESCs are connected to the ground terminal of the battery. The APM ground is also connected to the gound terminal of the battery (trough the black wire from the ESC no 1). So you do not need to connect the ground terminal from all ESCs to the APM since all ESCs have the same ground. As I said, if you do connect all black wires it will not do anything wrong, it's just that only one ground wire is required because all ESCs have the exact same ground.