[eluser]OverZealous[/eluser] @NachoF
I'm not really sure I can help you set it up. I started with a New Project from existing sources. NB allowed me to put the nbproject folder into a different location. There isn't too much more to set up.
NetBeans might have project templates, but I've never used them. It's really as simple as copying in the CI files, at any rate, and NB will immediately see the imported files.
I work out of a local directory, because I use Subversion to make changes safe, and I never work directly on production files. After a bit of work, I was able to set up my local Apache (included with OS X) and local PHP (also included with OS X, but I had to build and add several features) and point a virtual server to the working directory. This setup is awesome, because I can simply save my file, refresh and I can see it. If you use NB's remote setup, you can do the same thing via FTP or SFTP (by auto-uploading on save).
My project is big enough, however, that I made a custom PHP build file. I won't go into detail, but it lets me run a lint check on all PHP and JS files (catching typos early), compress all images, JS, and CSS files, and then hand it off to Unison to sync across either my Dev, Test, or Production servers as necessary.