Encrypt web.config including external appsettings and connectionstrings files
Web.config encryption with external files by using aspnet_regiis made my go crazy; but i found a way to do that;
you may check here for more details and code snippet
http://weblogs.asp.net/muhanadyounis/pages/encrypt-web-config-including-extarnal-appsettings-and-connectionstrings-files.aspx
hope this helps