STS: The members of the Alliance of Darkness have formed a tactical cooperation to further their nefarious aims. Although they mistrust each other they are aware of the advantages of cooperating towards a common, external goal.
STO: The Alliance of Light seeks to uphold the light even in the darkest of times in the galaxy. There is no formal structure. Its members cooperate intuitively and harmoniously towards spreading the light in the Galaxy.
When playing the Alliance of Light/Darkness you have some benefit that supports cooperation with players of your alignment and helps you when at war with players of the opposite alignment. There is also a penalty for switching alignment so the best strategy is to pick one at start and stick with that.