Entangle is the E17 app to edit your menus and iconbar and engage launchers. It doesn't creat and EAP files for you though, there is an editor for the format in the e_utils package. just check it out from their CVS and compile that, it's there somewhere.
And for the run dialog, the command is Exige. I'm not sure if it's part of the base distrobution or e_utils, but at any rate, that's what you're looking for
A good guide to enlightenment is get-e.org