Once Mii Maker is successfully installed, using it is virtually identical to using it on a real 3DS. The TechBloat guide confirms that "Once the necessary files are in place, you can launch Mii Maker through Citra, allowing you to create and edit characters similar to those on the original device".
: Use a tool like GodMode9 to dump the system title for Mii Maker as a .cia or .app file. citra mii maker download