CVI has its own API for User Interface development. It is based on the Windows API, but has richer features and is generally considered easier to program. If you have a CVI panel and want to call WINAPI calls on it, you can get the system handle of the CVI panel with GetPanelAttribute. However, what you are asking is can I use CVI functions on windows created with SDK functions like CreateWindow. The answer is no. However, you should be able to find equivalent functionality in the Windows SDK to do almost everything CVI does in a window created with CreateWindow. In your case, try looking at GetMouseMovePointsEx in the Windows SDK to get the mouse coordinates.
Best Regards,
Chris Matthews
National Instruments