Download 3DS Emulator-0.9.5.3(Citra)Setup.rar & Emulator3DS_PokemonX&Y.rar from this page.
Extract it by double clicking the .rar file and open the setup .exe file.
You will be prompted with the installation of the emulator, to proceed click next and accept plugins/addons if the installer cant find them. the installer will automatically install those files and will make a shortcut on your desktop of the 3ds emulator.
After the installation is done, its time to install the Bios - download it here (instructions on how to install the bios can be found of that page too.)
After you installed the bios you can open the emulator located on your desktop.
To play a game simply click file>open... and load and navigate to the .3ds rom.