When you configure your Report Server to use Integrated Mode there will be some changes in the web services.

There is a new SOAP endpoint, ReportService2006.asmx, that replaces ReportService2005.asmx. In integrated mode all calls to ReportService2005 will result in an "operation not supported" exception.

The ReportExecution2005.asmx end point will still work in both integrated and native modes. However, because he reports are stored in SharePoint, the report server paths are no longer used.

A set of SharePoint proxy end points have also been added for working with a report server in Integrated mode. Using these endpoints, SharePoint will handle the authentication between the SharePoint server and the report server.

The ReportServiceAuthentication proxy endpoint is used for authentication with a report server when an application is using Forms Authentication.

Features Supported by Reporting Services in SharePoint Integrated Mode

Using SOAP API In a SharePoint Application

*Update*

So far, I have found that the biggest change in the endpoints is that the ReportPath for web methods that expect one is now a SharePoint path. Other than this I haven't had to make any changes in my web service calls.