By default the code is applied on the entire website. Use this feature to restrict the pages on which the code shows up. For example, the settings from the left screenshot will apply the code on the entire website, except on the pages with the URL containing the word "category". You can add further constrains to match exactly the pages you want.
On multisite WordPress installations any custom CSS/JS/HTML code written in the main subsite can show up on all the other subsites, if the "Apply network wide" option is enabled. The Simple Custom CSS and JS Pro plugin needs to be activated on all the subsites where you want the custom code to show up, but the license key doesn't need to be activated on each of the subsites for this functionality to work