NOTE - Not Available at Basic subscription level
Showing your PDF plan in an orientation that makes it easier to work on, rather than the orientation it may have come in, makes a lot of sense.
To rotate your PDF plan orientation in ArcSite, you can do so during the initial uploading process.
There are a number of small steps involved with uploading the PDF. During the 3rd step "Pending Publish" click on the More Options icon and choose Rotate.