Search Engine's user interface has been designed to be simple and easy to navigate. At the top of each page, a gray navigation bar allows you to jump to the Sample Search Forms, Category Editor, Ignore List, Reports, or change Setup Options. At any point you may navigate to other sections of the program, but be cautious to save your work before you do so. When working with data on a page, no changes are recorded until the "Save" button is clicked.

If you accidentally go to another page or click "Cancel", you can usually click the "Back" button on your web browser, and it will remember what was last entered in the form. This functionality may or may not be available, as it is dependant on your web browser, not Search Engine.

When browsing through the Category Editor, you can use the Keyword Search function to narrow down the number of entries to search through. Search Engine remembers your last Keyword for a while if you leave the page and return, and it may be confusing at first to only see one or two records. To show all of your records again, use the "List All" button, which resets the Keyword Search.

Search Engine needs to have categories defined to tell it where to search on your site. When the program is installed, a default category will be created. The program tries to determine your web root and sets up the category to search your whole site. For some sites, this might be too much content to search, and you'll want to reduce the scope of the category.