Update scripts for Themes/Plugins

Hi,
I was wondering how I update themes (or plugins) convieniently.
Some parts of themes have to be configured in the wordpress backend ,like the position of widgets.
I thought maybe their is a way to put this in code. Like a file update.php which is called after I deployed the new version where I can setup all these things.

Or for plugins. I need to update a database structure or something like that.
The background is, that I try to build a environment where I can use a development, staging and live server without using any 3rd party tools. Just copy source code 😉