The Red External LED mirrors the true Arming LED (that you can see through the Flight-Controller's white plastic case). Obviously, if the true one isn't lighting, neither will this external one.
The Green External LED mirrors the (tiny red) true GPS-Fix LED (on the bottom of the GPS-Module).
There is also a yellow LED that signifies various calibration modes.
The pinouts for the 4-pin black DuPont External LED assembly in here.
http://quadcopter-robotics.blogspot.com/2015/01/nova-rebuild-apm-internal-component.html
To test LEDs (to make sure a non-lighting one isn't burnt-out): After documenting plug orientation, you can disconnect it from FC. Then apply (properly polarized) 5 volts on the proper 2-pins sets ... to test each external LED. Do not reverse polarity or you might blow an LED.
JW57RC (in RCGroups forum) manually traced-out his particular LED assembly, and created this schematic
As for the (non-keyed) orientation of the black 4-pin Dupont plug into the Nova/Cheerson v252 Flight Controller ... there is only one way it must be plugged in. It also appears there are 2 different ways (because different wire colors were used), but in actuality, there is only one (it's all the same electrically). On my newer Nova v5.0 FC, it is orientated as above.
On my older Nova with v2.0 FC (below), it uses these wire colors. My best recommendation is to document your current stock and working way, and keep it that way. If it gets lost, you can match one of these two.
Here is a video about it converting them to work on a full APM FC.
Yet another pic that a helpful RCGroups forum member posted.
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