If the word template mean the joomla template (the look, the themes) and that you want to have the new template as default for a group of website, you have to go in the back-end of each slave site to select the new default template.
I don't know if you have shared the templates directory but if this is not the case and that you have decided to have speicifc templates directory, you will also have to go in each slave site and re-install the template.
Concerning the menu, you will also have to go in each slave site and rebuild them.
Concerning the modules, if you have installed a new module and that you have configured and activated before installing it into the slave with the "JMS Tools" then you will have the same module pre-configured in the slave. If you have created a slave that group a set of children then you can propagate the installation.
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