Eclipse is mostly geared towards working with files in projects in your
workspace - the Open File... allows some editing functionality of
external files, but many useful features may be missing. I'm not
familiar with the PHP plug-in, but it's possible that this is the reason
that line numbers are not showing in your editor. Eclipse does not
currently support opening external files by launching from a file
association. There's a long standing enhancement request open to add
this feature, but it's not likely to be done any time soon.
Basically you'll probably be better off learning to make use of your
workspace... the PHP plug-in should provide some help or tutorials to
help you get started with developing with Eclipse.