There are two main manuals: the Flora-2 User's Manual and a manual describing the packages that are not part of the core system, but are important additions and are distributed with the system. There is also a tutorial that covers the main aspects of the theory behind Flora-2 as well as introduces the key features of the system.
Furthermore, Ergo tutorials on the Coherent Knowledge's Web site are also relevant. The ErgoAI Tutorial is a gentle introduction to many syntactic and semantic features of Ergo, and much of it is applicable to Flora-2. The second tutorial, Capturing Real World Knowledge in ErgoAI, explains the process of development of a knowledge base for a real world domain (using the laws from California Driver's Handbook). Almost all of it, including the supplementary materials, applies to Flora-2 as well. This tutorial uses only the basic features of Ergo and Flora-2, and could serve as a good introduction into the subject.