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Its bad because when they submit the link to 400 search engine submission then you will receive same number of spam messages to your mail. Many search engines don't like submission from an automated submission tools as the creator don't care about the rules and creator just want to list as many engines as possible. Normal tool access search engine submission script without going to website. This results in receiving lot of spams from the tools then your submission will be ignored if search engine find out that you used such a tool to submit your site.

As my suggestion both are good for getting ranking but for some limited time only. If you want ranking for permanent than go with manually will be good for future

It's a waste of money. Search engines will find your site just fine - even if you never create a webmaster tools account and submit your sitemap. Just link to it from Google+, Facebook and Twitter and the only ones that matter will find your site/pages soon enough.

Search engine submission will not help your pages rank at all. They may get discovered slightly earlier, that's all.

Don't go for any paid backlinks activities especially paid directory and search engine submission strategies. It might be give the instant backlinks and value to your website. But It should affect your site authority and rankings in some other days due to Google Penguin algorithms.