Try this
yourCustomAlert.center = self.view.center;
Inside your scrollView
first get visible Rect of scrollview
CGRect visibleRect = CGRectMake(myScrollView.contentOffset.x, myScrollView.contentOffset.y, myScrollView.bounds.size.width, myScrollView.bounds.size.height)
then get it's center
CGPoint centerPoint = CGPointMake(visibleRect.size.width/2, visibleRect.size.height/2);
then set your alertView's center
yourCustomAlert.center = centerPoint;