PCSX2 has the first run configuration wizard to help you with configuration. The emulator will automatically store all settings, memcards and any new configuration related files in your My Documents folder if you used the installer, or in the same folder where pcsx2.exe is located if you downloaded the binary version.
Open downloaded zip file and extract PCSX2Fx_Settings.txt and shader.fx files in the same directory pcsx2.exe is located. You can change some shaders' settings by editing the PCSX2Fx_Settings.txt (the file contains all the needed instructions). External shaders should be used with caution because some of them may potentially have an enormous impact on speed. Note that you can use external shaders even with GSdx software renderer, which is the best way to get higher visual quality in this rendering mode.
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