Its really hard to find a tutorial to do this as most information relates to Xcode 3. Answer below may help some people.
I sourced most of my information for the ans
@bennythemink Your answer is really very much help full but I want to add some more things in your answer. When we copy xcode predefine template than this key contains
Ancestors
com.apple.dt.unit.storyboardApplication
this value. When we use this key value in Custom template of xcode it will create AppDelegate class by default. Which we can not move to folder only we can shift it into group. So i suggest to add this:
Ancestors
com.apple.dt.unit.objectiveCApplication
com.apple.dt.unit.iPhoneBase
com.apple.dt.unit.prefixable
value in Custom template so that we will have fully empty template in which we can do any custom stuff.