What are .cia files?
Basically they are like WAD files in WiiScene. They can be installed into your 3DS and be permanently there, just like if you download a title from the eShop. It is only recommendable to install theses in emuNand, as installing something on your sysNand could be dangerous. You can install 3DS games (converted to cia perviously) and forget about headers to be online. And they are installed on your 3DS SDcard and not on your flashcard's.