1) there is only one installer for both upgrade and new installation
2) The installer will walk you through the steps, make sure to have a full database backup first.
If you have a large database I recommend setting the recovery model to "simple" and shrinking the database.
3) The only one so far is this: http://www.lansweeper.com/forum/yaf_postst3453_Problem-with-HyperV-based-virtual-machines.aspx
But it is unrelated to the scanning server.