Hi Davide,
I ran into the same issue myself a little while ago!
You can now override individual layouts from within your template. Default layouts are in the /layouts/ folder and you can override them in your template the same way you did previously. For example, to modify the blog item title layout copy:
layouts/joomla/content/blog_style_default_item_title.php
to:
templates/*your template*/html/layouts/joomla/content/blog_style_default_item_title.php
For further info you should check out: http://docs.joomla.org/Sharing_layouts_across_views_or_extensions_with_JLayout
Regards,
Seth