There are two (2) ways to access the settings for your projects in the Site Audit tool:
1. From the Site Audit dashboard.
Click on the menu icon inline with the project you're wanting to edit:
2. From within the project itself.
Click on the settings icon in the top right-hand corner
Then click on "Open project settings"
Once you have made the changes, click "Save". Note: You will need to click on "New crawl" in order to account for these changes; so these updated settings will be used from the next crawl, but they are already saved, and past crawl(s) will not be changed in any way