Keep your frequently used commands in your worksheet. Since the worksheet gets saved automatically, your commands will be available next time you open Eddie. This is a more persistent and manageable form of a shell history file.
To keep the worksheet clean and have it only save commands you typed in and want to reuse later, use Undo to clear out output from shell tools, compiles, etc.
You may reopen all the files you worked next time you run Eddie - before quitting Eddie execute:
Windows -oAfter starting Eddie, select all the File 'xxx' lines and execute them. This will reopen all the files you worked on last time you ran Eddie.
Unlike MPW, Eddie currently only allows shell comand execution in shell windows. However a worksheet is only a Command-0 keypress away which makes it easy to quickly use shell commands.