Easy method is to download the freeShop cia, install that, then grab encTitleKeysUpdater cia and install that, then run encTitleKeysUpdater, Update encTitleKeys.bin with that app and then launch freeShop.
The harder method would be to use either That ISO Site or That Chaos Site to find a cia of the game you want, download that, transfer to your 3ds SD and then use FBI to install it. I only recommend this method if it doesn't show up in freeShop.
The hardest method is to download a .3ds file from That ISO Site or That Chaos Site, then convert to cia and then install it.
If you want to make backups of your own carts and install them, you can use Decrypt9 to dump a physical cart to .3ds, and from there convert to cia and then installing. Currently this requires using a PC to convert to cia, but I believe somone in the forums was developing a program to do it straight from 3ds, meaning in the near future (if it isn't already done) you can simply dump the cart, and then also convert it straight from the 3ds.