If I have:
<div> this is views/layouts/main.php <?php echo $content; ?> </div>
Then when ?r=mymodule/foo/bar is called, the above $content should get the output generated by the mymodule layout:
<div> this is modules/mymodule/views/layouts/main.php <?php echo $content; ?> </div>
where the above $content gets it value from modules/mymodule/views/foo/bar.php with the help of FooController::actionBar().
So note, nesting is wanted, not overwriting the global (application's) layout.
Say the modules/mymodule/controllers/FooController::actionBar() action generates the output "Hello world", the entire output should look like this:
<div> this is views/layouts/main.php <div> this is modules/mymodule/views/layouts/main.php Hello world </div> </div>