For your own module, use a custom .tlk with a unique name. Put other custom content into .hak files with unique names. These files can coexist with others in the tlk and hak folders because they will be invisible to every module except yours. Use Module Properties to specify which file your module uses.

You can also use .hak files that have been installed for other modules, as long as you don't change them.

You can mess up other modules by putting files in other folders, especially the override folder. There are exceptions to this rule-of-thumb, so ask for more advice if need be.