When everything has its place, that means already half the work is done.
While keeping order is important, it is equally important to feel at home in your environment, whether text or graphical. The text environment is controlled through the shell setup files. The graphical environment is primarily dependent on the X server configuration, on which a number of other applications are built, such as window and desktop managers and graphical applications, each with their own config files. You should read the system and program specific documentation to find out about how to configure them.
Regional settings such as keyboard setup, installing appropriate fonts and language support are best done at installation time.
Software is managed either automatically or manually using a package system.