Why not to use automatic directory submission software?
Basically auto submitter can be seen as spam by the search engines, especially if they are submitted many times in a short period of time. If that is the case Google will ban the site. The best way to have a site indexed is through linking and perhaps part of your fee could be used to buy the appropriate links.
As proof, point your customers to the Google Webmaster Guidelines where they explicitly say that they do not like auto submitter
http://www.google.com/support/webmasters…
Don’t use unauthorized computer programs to submit pages, check rankings, etc. Such programs consume computing resources and violate our Terms of Service. Google does not recommend the use of products.
Your site to be banned by Google and the other search engines, use manual submit instead of these automatic submission tools. After-all, it is clear in the guidelines.
No need to submit 1000 directories to your site. manually 5-10 high quality directories in a day, it is enough for website. Manual submission is more reliable and relevant than the automated ones.