Zend Studio for Eclipse is supporting the latest Zend Framework and you might need the latest library code referred in your updated projects.
The way to use Studio for i5/OS with your i5 is to use Remote Debugging. This will allow you to compose a script on your PC and run it in Studio using the php engine running on your i5. You will need to do this to access the i5 Toolkit Functions such as i5_connect(), as well as the ibm_db2 extensions, such as db2_connect().
This article explains how to use the Zend Debugger to debug command line PHP scripts without a dedicated web server, i.e. how to start a debug session from the command line.