Well there is a question that most all people that submit links to directories do not know or understand and even some directory owners just starting out in the business may not know.In short deep links are internal links to the website.
For a link submitter
The main thing that link submitters need to remember and do, is properly plan the extra internal links that they want to submit. The deep links (internal links) should first and foremost be to your most important products and services that you offer, as that's probably what is the most important for you to promote.
So anyone who is submitting links to their website should consider in advance what internal links that they would like to submit if the directory they are submitting to accepts them. This should be planned carefully in part of you link building campaign. After all the whole purpose of building links and promoting your website is to drive quality targeted traffic to your website's products and services and also for the search engines to find and index your website and you products and services pages.
Most directories that accept deep links, have a range of 3 - 5 which is ideal, anymore could end up looking like spam, not only to directory visitors but to search engines as well. So for many reasons it would be best to limit your deep links to 5 when submitting a site.
Some directories also allow descriptions with the deep links which are even more beneficial as for example if you have a product or service page you wish to add as a deep link, you can also give a complete description of what it is.
What many link submitters that already know about using deep links do, is to write up a list of various internal links that they wish to use for submission and write up proper titles for each along with descriptions. Then when submitting to directories that accept deep links, they can just copy and paste the links that they wish to use and if descriptions are allowed they can do the same and easily edit and modify each one for unique descriptions.