These examples assume that there is a chapter called "Chpater 2" in the publication and it is set to open in a new window.
To set a new chapter window to appear at 20% across and 40% down the display, and then display the first page in that chapter:
// Find the chapter object to modify
var Chap = GetPublication().FindChild("Chapter 2");
// Set the initial position to 20% across and 40% down
Chap.SetInitialPositionPercent( 20, 40 );
// Open the chapter by going to the first page in it.
GotoPage( Chap.GetFirstChild().GetName() );
To reset the initial position of the chapter to the defaults specified in the editor and open the first page in that chapter:
var Chap = GetPublication().FindChild("Chapter 2");
Chap.SetInitialPositionPercent(-1,-1);
GotoPage( Chap.GetFirstChild().GetName() );