I'd probably use AnnotationXY for it. It can be set to use screen coordinates or axis values.
For screen coordinates based approach, set:
annot.Style = Rectangle
annot.Anchor.X = 0; //sets anchor to top left
annot.Anchor.Y = 0;
annot.LocationCoordinateSystem = ScreenCoordinates;
annot.LocationScreenCoords.X = mouseX;
annot.LocationScreenCoords.Y = mouseY;
annot.Sizing = ScreenCoordinates
annot.SizeScreenCoords.Width = 100;
annot.SizeScreenCoords.Height = 100;
when you then grab from the edge of the annotation or drag it to other location, SizeScreenCoords and LocationScreenCoords get updated, and you can use that info for further data analysis. You can always convert the screen coordinates into axis values (data values) by using axis.CoordToValue method.
For axis values based approach, take a look at properties
annot.Sizing = AxisValueBoundaries
annot.AxisValuesBoundaries.XMin, XMax, YMin, YMax