I'm not sure why you are not getting "Update Template Files" dialog from DW, but as a test, open the index.php in the root of your site and change the copy right and upload the index page and see if you see any changes.
In regard to changing the left navigation color, you will need to update this line of code:
div.style.cssText = "background-color:#3375A2; color: white; border-top:0px;";
which is in the Main.dwt.php file in the Templates folder.
Let me know if you still have any other questions.