Instead, clone the templates you want to have customized variants of. Then change their names and the information in them. Finally, put them in the appropriate location in your account's Library/Application Support folder, specifically:
In XCode 4.5 right click on project, click Show File Inspector, then change Organization name in the file inspector's second tab (Project Document group)
更新:
As @carbo18 noted, it's proably better to create the directory ~/Library/Developer/Xcode/Templates/File Templates/Source and put your custom templates there. The best way may be to use as base one of the ones in /Applications/Xcode.app/Contents/Developer/Library/Xcode/Templates/File Templates/Source