The IDE frequently runs command-line tools such as gdb and mkefs behind the scenes, but PhAB and the IDE are separate applications; each runs in its own window. You can create files, generate code snippets, edit callbacks, test your UI components, etc. in PhAB, while you continue to use the IDE to manage your project as well as debug your code, run diagnostics, etc.
PhAB was originally designed to run under the Photon microGUI on a QNX Neutrino host, but the phindows (Photon in Windows) utility lets you run PhAB on a Windows host as well. The IDE lets you see, debug, and interact with your target Photon application right from your host machine as if you were sitting in front of your target machine.
In most respects, using PhAB inside the IDE is the same as running PhAB as a standalone application.