It depends on the used layout. ALERTS should be above main content --- . But it is possible that with so an outdated theme it works differently way. I don't think so if it is moving with your changes...
On other pages there is the header or something like that, put it under the header itself (I mean there was the banner top image or something like that. Directly above
You can put in some HTML tags but I think that divs are outputted from this shortcode.