App Scan scanning is based on URLs and Domain. So if u want to scan only few parts of an application then go for Automatic Explore Only Option and then remove unwanted URLs after that go for testing only drop down menu of the green scan button.
Other way is manually explore the application and during that time only go to the portion that u want to be tested.
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For AppScan there is no difference between SSO application or any other web application. Just make sure to fixed userid and password in parameter and cookies. AppScan won't help you to find SSO integration vulnerability.
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