If you want to track the position of the mouse pointer, just capture the WM_MOUSEMOVE event in your message loop. The X position will be in the LOWORD portion of lParam, and the Y position will be in the HIWORD portion of lParam.
If you're trying to move the mouse to a specific co-ordinate, you might want to investigate using the following:
::PostMessage(hWnd, WM_MOUSEMOVE, 0, MAKELPARAM(xPos,yPos));
I'm not sure how well that will work, if at all though. So, if anybody else has a better suggestion...
By the way, MSDN is a really good resource for this sort of stuff. 
