Before diving into the installation, it helps to understand why a special approach is needed. The Nintendo 3DS does not run DSi games natively in its standard 3DS mode. Instead, it boots into a hardware-level backward compatibility mode, effectively turning your 3DS into a DSi temporarily.
Save the settings and click "Flipnote Theatre" to browse thousands of community-made animations just like it was 2010. To help tailor this setup, let me know: What is your 3DS console? flipnote studio dsi cia work