'acquisition' is the product of a subconscious process very similar to the process children undergo when they acquire their first language. It requires meaningful interaction in the target language - natural communication - in which speakers are concentrated not in the form of their utterances, but in the communicative act.
The "learned system" or "learning" is the product of formal instruction and it comprises a conscious process which results in conscious knowledge 'about' the language, for example knowledge of grammar rules. According to Krashen 'learning' is less important than 'acquisition'