cyskye Yes, you can override layout files via local folder of template.
For example, the override file for article page locates in:
[your_site_root]/templates/ja_blockk/html/com_content/article/
You can override this by copying this folder and paste into local folder:
[your_site_root]/templates/ja_blockk/local/html/com_content/article/
and customize files here.
It will not be affected when you update new version of template.