I gave up on eclipse the first day I tried it while working on a PHP project. I tried to open a plain text file in the project and from the project explorer(or whatever it's called) and it opened in notepad instead of an editor window in eclipse. I knew at that point it wasn't for me.
Maybe things have changed since then, but I haven't bothered to try it.
Eclipse feels like an OS in some respects due to the amount of configuration options there are. Eclipse has file extension to editor mapping. You can map .php files to an Eclipse editor, but it may not be the default. If you installed the PHP Plugin[1] for eclipse, I'd bet that your .php files would then open in it's editor instead of the system default.
Maybe things have changed since then, but I haven't bothered to try it.