Basic subdirectory search-replace is controlled from the main window toolbar or the Advanced Tab in the script editor.
As of v 4.6 you can also limit how deeply the program will recurse within subdirectories. See the Special Registry Switches topic and scroll to the ' Limit Subdir Recurse Levels' section. Alternatively the switch can be set using the special configuration utility on our www site. Visit the Search and Replace page to download the utility.