Create a Script for "Install ScriptUI Panel" without having 2 windows.

Typically I'd do something like this. You need to check if AE is giving the script a panel (i.e. this) or not then either add to that panel or create a new window if it isn't running as a panel.

function main(thisObj) {

	var renderWindow;
	if (thisObj instanceof Panel) renderWindow = thisObj;
	else renderWindow =  new Window("palette", "Tool", undefined, {resizeable:true});

	// could also write it as
	//var renderWindow = (thisObj instanceof Panel) ? thisObj : new Window("palette", "Tool", undefined, {resizeable:true});

	var panelRender = renderWindow.add("panel", undefined, "QUEUE");
	panelRender.orientation = "row";
	var renderButton = panelRender.add("button", undefined, "OPEN APP");
	renderButton.onClick = function() {
		$.evalFile(File($.fileName).path + '/Tool_v001.jsx')
	}
	
	if (renderWindow instanceof Window) {
		renderWindow.center();
		renderWindow.show();
	} else {	
		renderWindow.layout.layout(true);
	}
}
main(this);