I think they mostly use the communication that falls under the categories "available to anyone" and "doesn't short out immediately near a wizard", which pretty much boils down to a very simple landline telephone.
Plus, I think they simply visit each other or meet up in Edinburgh to talk. The nevernever does make this fairly easy.
Changes Spoiler:
Harry used a communication stone to get in touch with Ebenezar. It seemed as though something like that was pretty uncommon. Then again, any number of wizards who know each other well might have things like that.
and on a sidenote:
link (http://modmyi.com/forums/attachments/native-iphone-ipod-touch-app-discussion/108771d1224045646-feature-comparison-between-stone-iphone-stone.jpg)