How to create a custom theme layout


I am trying to create a multisite where users can create their own account/web page. I would like to be able to customise an existing wordpress theme and make it the default theme for the user. For example, I want the default them to be preconfigured with widgets such as Skype and Google Map. So when a new user signs up for a new account, the site that they get will already consist of the Skype and Google map widget in the default theme. I read that we can use Pro Site plugin or THeme Manager Plugin to create a custom theme layout. However, I cannot find any such documentation explaining how to do it. The usage documentation for the above 2 plugins do not explain how to create the custom layout for the default them. Can you please advise.

Thank you.