I think with Custom Theme Tools you can. I haven't personally tried it but I know it has the function to do so. Anyone who has done it can confirm? Also I heard YATA is better than Custom Theme Tools but I don't know if it has the function to convert custom themes to cia. Again some confirmation from someone who has tried would be appreciated.
I have mixed success applying themes on my New. Sometimes it works and sometimes it doesn't. I've only used Cubic Ninja to install themes in the past. It worked most all of the time if I power cycled the New 3DS first. Also when transferring the theme data via FTP it was important that I closed my FTP client before the 3DS' FTP server.