Excellent... I was missing the updating bit.
I also did the cloning thing. Presumably this is done just in case I mess up and need to get back to the default set.

Anyway, thanks for the help... much appreciated.

P.S.
I just looked back at sys admin >> templates and noticed you can actually edit the templates and submit the changes of the clone.
You can only view the defaults.
All is clear.

I wanted to add some of my own links to the Main Menu.
After rooting around I figured I had to edit the system_block_mainmenu.html file.
So I edited the file on the server adding the following link just after the main foreach block:
<a class="menuMain" href="<{$xoops_url}>/pcs/Management.php">Management</a>

Nothing happens.

Now, if I then view the template via the system admin/ templates route my new line is not there.
If I open the actual file on the server again my addition is still there...?
Could someone please tell me what am I doing wrong...?