Well to play .3DS format, I'm going to assume that OP has a flashcard. And since well gateway is the most popular i will use that example for this post.
With a .3DS rom it needs to be played from emuNAND or 'gateway mode' if you don't bother with emunand. To boot emunand or gateway mode you must have the red card inserted right? So you may as well just put it on your flash card and press select and navigate to the rom if the red cards already inserted, right?
Creating .CIAs are much more involved than the steps i posted above.