This has been discussed many times before in the search engine forum here, but I highly-recommend you submit to the major search engines by hands. It is frowned upon by search engines when you use programs to submit your sites. Unless you are submitting/handling a large quantity of sites, I say steer clear of them.
Actually I wasn't so much concerned with the major search engines and directories as I am with the specific ones.
All I am doing is forming coalitions with certain search engines, directories, and PR news sites to submit in. No one else would have access to this submission process other than a few I work with and myself.