If you are using xyscan for the first time I strongly recommended that you take a couple of minutes and go step by step through this documentation. At least you should read the following chapters of the documentation: Introduction, Loading Plots & Images, Moving the Cursor, Setting Markers, Scan Settings, and Scanning. When done, use a good quality plot where you know the exact coordinates of the data points and run a scan to see for test.
If you were using xyscan (version 2) before you should be able to get familiar to the new interface and features rather quickly. Have, at a minimum, a look at the What's New section.