First you have to install properly last version of NetBeans . After go in Nautilus where are your php files, right click on a php file, select Open With > Other application and you should find there NetBeans. Open with it.
If still you have problems, go in
/usr/share/applications/ and create with root privileges a
.desktop file with next things in:
Exec=<command to run program - something like /opt/netbeans/run.sh> %U
Another way would be if you open a terminal and run:
netbeans [ options ] [ files ]
man netbeans for more informations.