Keep your frequently used commands in your worksheet. Since the worksheet gets saved automatically, your commands will be available next time you open Eddie. You can think of it as the Worksheet equivalent of the bash history.
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.
Instead of using the "Reopen documents on startup" setting, you may selectively reopen files you worked next time you run Eddie - before quitting Eddie execute:
Windows -o
After starting Eddie, select all the desired File 'xxx' lines and execute them. This will
reopen all the files you worked on last time you ran Eddie.
Unlike MPW, regular Eddie document windows do not behave like a full shell. You may of-course use the Execute command in any Eddie window. Alternately, you can also temporarily toggle any window into a full shell (and back) by clicking on the shell icon (or the corresponding empty space) in the toolbar and that way converting the document into a full shell with a persistent state, etc.