Content type node not overwriting the default node.tpl.php even if I have cleared all cache's
Initially, i say like not to override the original theme folder,

Create a sub theme of the base theme, in your case create a sub-theme of twitter bootstrap.
Then make the necessary changes in the sub-theme.

Enable only the sub theme.

And about overriding node.tpl.php file,
your approach is correct node--empresas.tpl.php, should over-ride the display of this particular node content.

Cross check machine name, Enabled theme, path of the overriding tpl.php file.