bliss is designed as a long running server application that applies rules to a music collection. There are two functions of rules; assessment, which is judging whether your music is compliant or non-compliant, and the suggestion of automatic or suggested fixes. This is the assessment and automatic fix cycle. You can read more about the assessment and fix cycle in the "First steps..." cover art tutorial.
The most important takeaway is that the file organisation rule works in the same way as the cover art rule. It follows the same assessment and fix cycle. bliss first assesses whether the files are stored in the correct place, then, if they are stored incorrectly, either fixes them or suggests a fix to you to execute manually.