The new window should appear in the centre of the screen by default. This is not configurable within the plugin and I can’t support modifications of my plugins as part of the free support I offer.
If you want to have a go at changing the position you can make a forked copy of the plugin with an edited version of the popup.js file.
The ‘left’ & ‘top ‘variables set the position of the window, and these depend on the screen height & width, and the height & width values set in the shortcode (‘w’ & ‘h’).
default:
var left = (screen.width/2) - (w/2);
var top = (screen.height/2) - (h/2);
as a simple example for a modification, you can make the popup appear 100px from the top & left corner of the screen:
var left = 100;
var top = 100;