The sample plugin creates a panel, which can be docked or floating by default. Panels are listed in View menu.
You can add new toolbar buttons programmatically - I suggest you look in ASCompletion plugin's PluginMain.cs to see how it creates buttons, menus and even associated user-modifiable shortcuts.
The project data are globally accessible as: PluginCore.PluginBase.Project
To track active project changes, see in the sample plugin how it listens to file-switch event. Likewise you can listen to ProjectManager plugin events "ProjectManager.Project":http://code.google.com/p/flashdevelop/s ... Main.cs#44
Plugin devs often get into FD by "sniffing" all the commands exchanged by the plugins that way.