Hi Steven,
If you want to use a cookie for the audit phase, while essentially skipping the crawl phase, you can do this use the Cookie jar and the Session handling rule.
- Browse your website in Burp's proxy browser so that the cookie jar is filled with the necessary cookies.
- Navigate to Settings>Sessions and then click on Open cookie jar. This will open the cookie jar where you can see the session cookies. Copy and paste the session cookies in a text editor.
- Under the same Sessions window, you will find the Session handling rules. Click on Add to add a new rule.
- Set a Rule description and then click on Add. Click the "Set a specific cookie or parameter value" option.
- Give the cookie name and value that you got from the cookie jar.
- Check the 'If not already present, add as cookie' checkbox.
- Set the scope for this rule. Click Ok, and you should be good to go.
Try this in the repeater tab. Send a request for the site without the cookie and see if Burp adds it to the request.
Let me know if this works out or if you need further help.