This has been made a lot easier from version 5.4.0.0 where you can use your own logo instead of the default KonaKart logo by simply replacing the logo.png file that contains the KonaKart logo directly under the konakartadmin webapp (the file is approximately 6KB in size). You must use a PNG file and the dimensions should ideally be the same as the KonaKart Logo which are: 240x60 pixels.

For example you can replace the KonaKart logo with your own logo as illustrated below:

KonaKart Admin Application - Custom Logo