I assume this can be done but how, I am talking you know aux, engines, shields. weapons energy, and no I dont mean transferring from one to the other but adding to the total amount, or at least making everything more efficient so it uses less energy ? are either of these doable ?

With certain kinds of gear/consoles/traits, yes your energy totals can be increased.

The red matter device from the collectors edition is the only thing I've seen so far.

You can, up to I think 125. However, it requires skill points spent in the right places and Consoles to add bonuses.

When they become available for you, putting points into the "efficiency" skills is like 1 skill point = 1 power level point. I think they are Commander level skills.

And unless they changed it, if you pick the engines as the reward from the Doomsday mission, it adds +5 to Wep/Shld/Aux.

There are items (consoles for the most part) than will increase the power levels in the different systems, and abilities (the Emergency Power to <system> line, for example).

In addition, the Starship Warp Core Training, Starship <system> Efficiency and Starship <system> Performance skills can all increase your power output.