Rather it is manual submission or auto submission, the purposes for search engine submission is to increase visitor traffic, exposure, link popularity, branding and the most importantly, page rank ( PR ) for your website within the major search engines. Manual submission creates higher inclusion rate than automated submission.
Many search engines, especially the highly valued search engines and directories, often requires sign-in and password confirmation prior for submission. With automated submission, this is not possible. Many of the automated submission services promise over thousands and thousands of search engines and directories submission and be submitted within 20 minuites or less.
In reality, most of those will be spam search engines submission and FAA/link farms submission to create temporary inbound links only. Major search engines dislike FAA or link farms sites and you will be at risk of being penalized. That is, having your website banned for good.