Well, I've only tried GemFX in conjuction with the ESOLauncher but I don't see why SweetFX wouldn't work the same way...
Move everything from the SweetFX_ESO folder in the folder where eso.exe is (in my case: C:\Program Files (x86)\ESO\Zenimax Online\The Elder Scrolls Online EU\game\client). After that it should work automatically (the ESOLauncher, as usual, doesn't have to be in the same folder, it can be wherever).
To uninstall SweetFX delete the files you placed inside the client folder (it's a good idea to take a screenshot of the client folder before moving anything to it so that you know which files to delete).
If you're on Win8, this thread might be related to your problem: https://forums.gamemodi.net/viewtopic.php?f=8&t=1964
In case you immediately crash when starting up the game; go into \Documents\Elder Scrolls Online\liveeu or livena for americans I believe and open UserSettings.txt and change the variable SET GraphicsDriver.7 "D3D11" to "D3D9".