But when I try to download the map after clicking the "Create atlas" button I get the following error: Unable to find SQLite libraries. These are required for selected atlas format.
Motokai, if you haven't sorted "Unable to find SQLite libraries"
this is how i got it work:
download http://files.zentus.com/sqlitejdbc/sqlitejdbc-v056.jar, and place to same directory where Mobile_Atlas_Creator.jar is located.

SQLite (optional)
Some atlas formats uses a SQLite database for storing the tiles. For creating SQLite database the additional Java library SQLiteJDBC is required. MOBAC has been tested with sqlitejdbc-v056.jar - newer versions should also work.
Installation of the additional SQLite libraries is pretty simple: Just jownload the JAR file and place it in the same directory where Mobile_Atlas_Creator.jar is located. Alternatively you can place it in any path covered by the JAVA search path. The next time MOBAC is started the SQLite library is loaded and can be used."