I use a software program that automatically submits my site's URLs to the search engines
The search engines have made it abundantly clear that it is not good to use automated submission programs. The fact of the matter is that these tools do not work very effectively any longer due to the different search engine workings.
How often should I submit my top URL's?
If they are in the database, don't submit unless you have made a considerable update.
Also, I read that they say you only need to submit your Top Level Domain. Is this true? How many URL's can I submit?
You do only need to submit your root domain to most of the larger engines and they will crawl the rest of your website. For AltaVista, submit all of your pages (manually), with 5 a day as a limit.
submits my site's URLs to the search engines
With the exception of a few, search engine submission is a thing of the past. To get your website in Google you need to obtain links, not through submitting, and the same can be done for others.
Jake, I heard a good quote on submitting to search engines the other day. I think it answers your question:
(Free) submission to search engines are like cathing flies with your toes – it can be done – but it will cost you alot of time.
Agerhart summed it up pretty well though, and I only want to add that don't bother doing re-submissions. The engines will in most cases pick your site up anyway. Spend your time on content development and directory submissions :)