This is just an update in case people come here looking for a solution to the same question.
First thank you to those that answered my call for help and gave me important pointers.
In XOOPS 2.5.4 templates seems (I write "seems" because I don't know if I have understood it 100% correctly) to be located as files in a folder and not in the database as was the method used earlier.
If you want to have your own theme and your own templates this is how it (seemingly
) works (it works at my end anyway):
This is based on a vanilla installation.
At the location my_site/themes you should find the following folders default, suico and zetagenesis
Add a folder for your own theme:
my_site/themes/my_theme
Place your files for your theme here, such as style.css, theme_blockcenter_c.html etc.
Then add a folder called modules:
my_site/themes/my_theme/modules
and add a folder for each module you want a template for (in this case the module newbb):
my_site/themes/my_theme/modules/newbb
Here you place your template files such as newbb_index.html, newbb_thread.html etc. You also make a folder called blocks
my_site/themes/my_theme/modules/newbb/blocks
where the block-templates go (newbb_block.html, newbb_block_author.html etc.).
When your folders are in place you can - if you wish - copy old template files into the new directory structure and they should work - as long as the version of the templates is the same as the version of the module you have installed.
Now, when I go to administration, templates and in the directory listing to the left clicks on my_theme, on modules and then on newbb I will see all the templates for that theme and for that module.
Clicking one of the template files it pops up in the editor window on the right and you can modify as you see fit and the changes carry through.
I
assume that XOOPS will default to the templates in the default theme if it can not find the module in your custom theme - it seems to do so here. This means that you only need the templates for the moule(s) you want to modify.
And therefor I suggest you keep the default theme at all times, so XOOPS have something to fall back to.
Now, I still have no clue as to what "Choose template" and "Forced file generation" etc does. Doesn't seem to do anything at all here.
I hope this will be of some help to someone.