Documents are, much as the name suggests, individual documents which contain a set of clauses. For example: a non-disclosure agreement.
Binders on the other hand are collections of documents which have been grouped together. For example: an outsourcing agreement with a pricing annex, technical annex, etc.
Every document in ClauseBase can be made part of a Binder. In fact, you are strongly advised to actively edit documents, and to only join them together into a Binder as the very last step.