big db for managing user files and settings
The first path is certainly the more conventional of the two, absent a compelling reason to break the system down into multiple schemas.  Something along these lines:

CREATE TABLE user (
  user_id INT AUTO_INCREMENT PRIMARY KEY NOT NULL ,
  user_name VARCHAR(50) NOT NULL,
  password VARCHAR(32) NOT NULL,
  status_code INT NOT NULL
) ENGINE=InnoDB;

CREATE TABLE user_file (
  file_id INT AUTO_INCREMENT PRIMARY KEY NOT NULL ,
  user_id INT NOT NULL,
  path VARCHAR(2000) NOT NULL,
  INDEX (user_id),
  CONSTRAINT FOREIGN KEY (user_id)
    REFERENCES user(user_id)
) ENGINE=InnoDB;

CREATE TABLE user_settings (
  user_id INT PRIMARY KEY NOT NULL,
  email VARCHAR(150),
  color VARCHAR(10),
  etc VARCHAR(255),
  CONSTRAINT FOREIGN KEY (user_id)
    REFERENCES user(user_id)
) ENGINE=InnoDB;