what method to bring open files into one as layers ?

There are scripts to load files into a stack, before opening them all into Photoshop.

You could run a Batch Action to save and close all open files, then run the Load Files to Stack script.

This may prove challenging to fully or semi-automate with all docs already open. 

CS6 may limit your scripted options as most people script in later versions and can't create or test scripts in older versions... But this can be done with a Batch Action in CS6, even if it is a bit rough.

It will depend on whether the files are flattened or layered.

Here I created a simple action for images that are not flattened. For flattened images remove or disable the first step. All files should be consistent, either flattened or ensure that any flattened Background image is converted to a floating layer:

I have set the modal control on the last step for an interactive save step as I didn't wish to save changes to all the open documents (file_2.png and file_3.png), I only wanted to save the final file_1.png document. If you don't care about saving changes to open docs then you would just record the last step with a "saving: yes" and not run in modal.

Then run the Action via Batch for all open docs:

Notice how the files have been opened so that the target document "file_1.png" is the last document processed, which will be the layered file that will be saved.

If there is any doubt or room for error in closing unsaved files, I would just run the action manually as many times as needed.

Good luck!