We apologize for taking so long to get to this but we have updated the Setting page to explain the reasoning behind the war and why the leaders are in their current positions.
As for your other questions,
-Energon color varies between players. Any canon colors are acceptable. Energon may also double as blood and as fuel. It depends on the context.
-Character designs are completely up to the player.
Thank you for your question and we apologize again for being so late.