Automated submissions is definitely not the way. Most quality directories have something known as a "captcha code" to prevent automated submissions, so even if you do meet with some amount of success, it would be in junk directories, that wouldn't really add any value to your site. Besides, when there are so many cheap manual submissions options available, it beats me to know why someone would even consider automated submissions.
Any autosubmission software can harm you - the only people who tell you otherwise are people trying to sell you an autosubmission service