I can't recall, are both surfaces the gasket mates against flat?.....if so it doesn't matter - ideally the gaskets should be replaced but if this is the first time the headers have been removed you should be ok.
Edit: just checked the manual, no reference to the gaskets being used in any particular orientation.
Cheers
Andy
www.MotorcycleInfo.co.uk and
www.MTS1200.info