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.
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.