If you aren't using original discs, you want the ISO plug-in available from the drop-down menu.
The only two options you'll probably want to change (apart from remapping the control pad) are the CD/DVD and the GS (read: video) plug-in. If you have five or ten spare minutes, read on, brave soldier. Download, run the installer, open the emulator, and you'll be staring down that very wizard. You can download PCSX2 from its official website with its most up-to-date plug-ins automatically packed in, and with a configuration wizard that walks you through the whole setup process. The Sony PlayStation 2.PCSX 2 is the only PS2 emulator around, and it's quite a masterpiece, despite being a bit of a bear to configure.