the result of copying plugins/features into that folder is not that predictable and hence not safe. Eclipse adviced to install plugins via "Install new Software" - it will tell you about conflicts (like different plugins use different version of another plugin" etc; or you need to install another plugin etc.) Otherwise I had situations when it didn't work and I got no idea why (had to read logs to figure it out).
Well, to install new plugin you have few possibilities:
1) "Install new Software" - you already tried it. Take into account that the list of plugins by default is limited here. But below the button "Add..." you can see "Available Software Sites" - this list is enhanced, and some of plugins you can find here". UPDATE: the process of installation is described here
2) With new Eclipse (Helios) you got new way to add plugins, so called Eclipse Marketplace (Help/Eclipse Marketplace...). This is recommended way to look and install new plugins.
Back to your problem - I think it is much more easier to download Java IDE for Java EE Developers, and install PHP Development Tools there. In Marketplace I selected Yoxos as source, typed "pdt" and found plugins related to PDTs (although I'm not sure there are all parts of it)