services like Submit Edge give you a list of all the directories they submit to, and usually you can take the matter up with the project manager. Whenever you outsource directory submissions you should always request a list of the directories they submit to (and pr if possible), and then go and check up on some of them later.
It's not really about whether anyone knows whether you do it automatically or manually, it's rather that automatic submissions usually imply a very poor standard of directory that you're going to be submitted to. It won't hurt your rankings, but it's not exactly going to help them either if you've just got your link on a couple thousand sites that aren't even listed in Google (many of them get banned because they apply blackhat seo tactics, or link out to bad sites - all because they don't filter their submissions).
I would prefer manual submission. It results better and work great. Submitter software are sucks, always spam
If you are using the service of manual submission sites, they usually provide you with a report. Stick with one submission company to minimize duplicate submission.