I have an R4.
To add an app, I connect the MiniSD card to my PC's USB slot and it adds it as a drive letter.
I dump the file into a directory I set up called "04 -- Homebrew" (00 -- Games; 01 -- Comics; 02 -- MP3s; 03 -- Videos, etc)
I boot the DS up, and navigate to the 04 directory and...