Sometimes little can be used as an adverb. "I'm feeling a little sick." (I'm feeling slightly sick) "I'm more that a little annoyed with you."
That's about the only rule I can think of. The rest is mostly idiomatic. For the most part, the words are interchangable.
You can have a small car or a little car and they're the same car. That car can have a small vibration in the steering, or a little one, and they are the same vibration. Something can be of no use or little use, but not small use.
Generally, big and little and large and small are considered opposites.