Although iOS 6 still doesn’t allow you to reorder the individual calendars on your iPhone, iPad or iPod touch directly, there is a handy workaround if you’re syncing with iCloud. Simply log into your account on the iCloud web site at http://www.icloud.com and select your Calendar from the list of options that appear.
In the web-based calendar list you will be able to drag and drop calendars to reorder them and changes made here will propagate to your iOS devices. If you’re using OS X Mountain Lion you can do the same thing from the Calendars app, but OS X Lion users will likely find that changes to the calendar order in iCal don’t always sync to your device properly, so doing this from the iCloud.com web calendar is generally the more reliable option.
Further, this is the only option available to Windows users, as the calendar ordering in Microsoft Outlook does not sync to iCloud at all.