Launch Universal-Updater from the HOME Menu, or from the Homebrew Launcher
Select the magnifying glass on the bottom screen, then search for PKSM
Press A while hovering over PKSM from the list of homebrew
Choose PKSM.cia to install to the HOME Menu, or PKSM.3dsx to install to the Homebrew Launcher
Wait until the app finishes installing
Exit Universal-Updater
You can scan one of the QR codes below to download and install the program using FBI. To do this, start FBI, then go to "Remote Install", then "Scan QR Code".
The PKSM wiki documents how to use the application.
Setting up missing saves
If your title is a 3DS game or official Virtual Console title, then your game should show up by default. If not, then some additional setup is required for PKSM to use your save. First, ensure that you have made an initial save in the missing title.