The way the OS is organized, may take a little getting used to, but there has been a LOT of thought behind it and it's much more logical.
Apple Menu:
This now contains system-specific functions which can be accessed at any time, from within any app without having to click to the Finder first. Most importantly, it contains Log Out, Sleep, Restart, Shutdown, and System Preferences.
App Menu:
In pre-X days, there were no rules for where certain functions would go. If you wanted to quit the app, you went to the File menu, if you wanted a preference you would go somewhere else, if you wanted information about the app you would to the Apple menu -- no logical reasoning behind it. Now App-specific information is located under the App menu: About this app, App preferences (what a concept), show/hide, and quit app.
File Menu:
Finally, app specific information has been removed from File menu which now only contains file-specific information: printing functions, open/saving/closing functions and so on.
My best advice to you is to abandon the old way and embrace the new. Much of what we knew in pre-X were kludges and hacks and didn't really make sense. To fully appreciate X you have to put all of that behind you.... not that I wouldn't like to see some changes, but one thing at a time.