If you're using Pepakura Designer 3, I would suggest using the 'Measure Distance Between Points' tool. Measure the distance between where you'd guess your ears to sit on the helmet, add maybe 2mm or so, then give it a shot. Failing that, yes, you could also scale the neck entry hole, though that's perhaps a slightly less-reliable method than measuring the helmet itself.
EDIT: if you can throw me a copy of the file I'll have a go at scaling it roughly for you.