Automated directory submission always generates issues like placing links in wrong categories with insufficient and wrong information. So, chances of rejection of listing increases.
I believe not manual. 1000 is a great number. With the help of soft, it is easy. But I don't know why you require a great number within a day.
People using submission softwares do nothing else but mass spam and really, that is so easy to spot. Most of the editors will not even bother to look at the website.
Manual submission is better and it does not take much time. Yesterday I submitted to 50 directories manually within 1 hour which is enough. Greedy webmasters and spammers are always concerned about submitting to 1000 directories within a very short time which is not a good seo technique.
I have found quality over quantity is far more beneficial, i like to hand pick my directories, and i use paid directories, they don t cost alot, and are human edited, check out my sig for 2 excellent directories.
As per my opinion manually directory submission is better then using any software for submission. Manual directory takes a lot of time in submission but it is more accurate in comparison of automated.