The documentation of Aptana 2.0 is poor at the moment, i did not find any docs on the new PDT PHP extension. Maybe someone has the same troubles getting php debugging to work – here is how i got it finally running:

I use the following system setup for local php development, testing and debugging:

OS:
Windows 7 (64-bit)

IDE:
Aptana Studio 2.0.2 with pdt extension

Server:
LAMP (ubuntu server 9, 32-bit) in a virtual machine (VMware server 2), PHP 5.2.10

To get a working debug configuration for php, the following steps are necessary:

• install the aptana PHP Debugger Binaries (PDT) via the plugin manager (my studio start page – plugins – featured plugins)
• install Zend Debugger on the server (i followed the tutorial found here) – make sure, that the IP of your development machine is added to the allowed hosts section of the zend debugger.
• add a new php server configuration in Aptana Studio
  Preferences – PHP- PHP Servers: simply add a new entry by giving a name and the http – address (e.g. http://ubuntulocal/)
• add a new debug configuration for your project
  click on the arrow next to the “bug” – symbol (debug configurations), setup a new configuration, choose “Zend Debugger” as Server Debugger and your configured server as “PHP Server”. In the “File” section, choose the path to the starting script of your app and check the right http-address in the “URL” section (“Auto Generate” is checked by default, in my case, this would result in a wrong url – just enter the right one manually). Finally make sure that ” Open in Browser” is active in the “Advanced” tab.

After saving the configuration your debug session should start by pressing the “Debug” button – the execution of the script should break at an automatically added breakpoint at the first line (you can change this behaviour in the debug configuration) and Aptana switches to the “Debug” view, where you can proceed with debugging.