FLVTool2 is a manipulation tool for Macromedia Flash Video files (FLV). It can calculate a lot of meta data, insert an onMetaData tag, cut FLV files, add cue points (onCuePoint), show the FLV structure and print meta data information in XML or YAML.
Overview of Cue Points: A cue point is any significant moment in time occurring within a video clip. Cue points enable you to access different segments of a video clip. With Flash Video, you can create and manage cue points in a variety of ways. This series provides a comprehensive guide to the use of cue points in Flash Video. In this first installment, you learn the basics of cue points and the requirements to create cue point data.
So in short FLVTool2 improve the quality of video what FFMPEG produced.