Does energy currently affect output?
Im 1.2k energy in the red on one planet,and when I edit my resources to return it to positive values, their is no increase in production, only a loss in the mine I set to a lower percentage.
So essentially what Im saying is, if energy being in the red brings negative effects, what are the effects?

I am not able to replicate what you describe.

On one of my planets with DS at 100%-
Total: M)11.891 C)5.980 D)4.527 E)-1.184

When I reduce to 90% and hit calculate-
Total: M)12.756 C)6.416 D)4.385 E)51

Everything increased except for the mine that I decreased production rate in. Seems to be working fine for me.

From what I understand is that negative energy lowers the efficiency of your production (decreased output). Basically, for every X amount of negative energy it decreases output X amount. When you manually decrease the production rate of a mine you have fewer points of production loss so it causes the output of the other mines to increase.

It is actually for every % of energy you lack for the required energy, your mines' output decreases by that %.

Sample:
all of your mines require a total of 1,000 energy for 100% output. If you only have 600 energy ( - 400), all your mines will only give 60% output.
Let's say your metal mine alone needs 400 energy. You can completely shut it down which will bring down the energy you need to 600. ( 0 )
This should allow the crystal mine and the deuterium synthesizer to both give 100% output.

Excess energy will not give you extra production.
You also have a basic income which is unaffected by the energy.

Hmmm fair enough. I havent checked the percentage yet, but on the planet Im talking about, it did not change the metal or deuterium outputs when I edited my crystal output so that the energy would go back into the positives. I would have though that 1.2k energy is at least a percentr :S