Benj, you can of course install eZ publish in www/ez_publish and keep there your development version. When you will done, you can use mod_rewrite rule (without moving files) or move your all files to root directory (www) or setup Virtual Host which will points to www/ez_publish. All possibilities will work. For eZ publish we recommend Virtual Host setup. Check documentation for more information: http://ez.no/doc/ez_publish/technical_manual/3_6/installation/virtual_host_setup
I'm gonna add to What Lukasz said that swiching from a developement setup to a production one is pretty easy...
I'd recommend that you develop on subdomains (dev.yoursite.com, admin.dev.yoursite.com), then just switch the virtualhost setup / host matching in site.ini when you're done.Everything should work perfectly.
