When you first open Eddie, the Worksheet window will come up. You can use it for normal text editing, just like any other window. In addition, you can use it to execute commands, because it is a Shell window. You may have multiple Shell windows open, you have only one Worksheet though and it has some special characteristics. Typically, you will use the Worksheet window to run make, execute small shell scripts, etc. Check out the Shell window chapter on details about executing commands in a shell window.
A Worksheet is a document located either in the ~/config/settings/Eddie/ directory or in the same directory as the Eddie application. You may choose one of the two to serve as the Worksheet source directory in Application Settings / Shell Windows. A Worksheet is automatically saved by default when Eddie quits. When you execute the CloseAll command (Command-Option-W), the Worksheet stays open. If you close the Worksheet, you may reopen it by pressing Command-0. Usually the Worksheet will be the main and only shell window you will use in Eddie, even though you can have as many shell windows open as you like.