Here's two places you can get custom themes and some additional notes on them!
For themes found on hShop, they must be installed with the application FBI on your 3DS. (
Theme Installation information). This Theme Installation Information page on the hShop website has some info on it. To install themes from hSHop, open up the FBI app on your 3DS. scroll down to
Remote Install and press A, select
Scan QR Code, scan the QR code found on the hshop themes page, finish the prompts on screen. Once installed, go back to your home page and find the Theme Installer Icon on your homescreen - it should show up as a "new software" on your screen. Open the installer and follow on screen prompts. Once it has finished installing you can apply the theme from the Anemone 3DS Theme Manager application.
To install themes from Theme Plaza, open up the Anemone 3DS Themes Manager. As shown on screen, press
R to
Scan QR Code. On Themes Plaza, hover over the image to show the QR Code for the theme, your 3DS will show "downloading". Once downloaded you can apply the theme from the menu and follow the on screen menu to get back to the main home page.