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.
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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.