Hello,
First, do not change anything inside the Default template directory.
Create another directory, copy all css inside this directory
Now you can just copy the file you want to change.
For example
Default
header.php
Mytemplate
css
header.php
The header will be overrided
Like that if you want to update the solution, it will be better for the maintenance and you can do all that you want inside this files. Sames approach for the module and files directory (respect the structure)
About your question
I do not understand what you want to do. Inside the admin you can select where you want to display a module.
The module page manager is only created to display the content information.
The best approach if want to do something is to create your own module and work inside.
Look the bm_shopping_cart inside the the boxes directory, you will have all the information you must need.