In jEdit many plugins supports dockable windows. These windows can be docked on the sides if the jEdit window or use as floated. LilyPondTool provides a couple of dockable windows:
the PDF viewer window, for quick preview of the score featuring point-and-click support
the Virtual Piano window, for quick typing of notes using the keyboard, the mouse or an external MIDI device
the Instant Help window, for a quick overview of the currently selected LilyPond command or property,
the MIDI Player.
Also, LilyPond uses other dockable windows, provided by other plugins:
the Error List, for reporting parsing errors (recognized by the embedded quick parser) and the errors reported by LilyPond,
the SideKick, for the structure browser,
the Project Viewer, that lets you organize your files into projects and set one of them as main file
The position of all dockable windows can be set in the Utilities>Global options>Docking menu or by clicking on the littlle arrow at the top-left corner of the dockable windows.