If your sitemap is in a custom location, or you have more than one sitemap, you can edit the project settings to let the crawler know where the sitemap(s) can be found. This option is only available for Basic Suite accounts or higher.
First, open the project settings. From there, navigate to the tab "Advanced analysis" and open "What to analyze" > "Sitemap URLs". Here, you can enter the custom location of your sitemap(s). The settings are saved automatically by clicking outside of the text box.