apparently the OP wants to install the games to the sdcard using the computer. as far as I know this cannot be done by any means at all, as the info required to do this is on the 3ds itself.
it's the same reason you can't just transfer a sdcard to a new 3ds and have the stuff on it work. you need info from that 3ds to perform the install, even with sigpatching.
Exactly why I suggested Boop, the OP did specifically ask about installing CIA files. Freeshop works. And for CIA, files Boop works well.. I miss the socket punch android app though.