I modified some files in the default template in
components/com_virtuemart/assets
components/com_virtuemart/views
How can i prevent that automatic software update overwrites my modified files ?
For template file changes you should use template overrides: see http://www.ostraining.com/blog/joomla/overrides and also http://docs.virtuemart.net/tutorials/33-templating-layouts.html
For css changes add your changes to the Joomla template css are maybe into a custom.css file, adding
Same with any js file changes, make a new file and add a link to the file in your template's index.php