Once I am satisfied with the layout, I flatten (merge all) and save it as a .tif file. If you are going to be taking them to a printer, this is the format you will want to use. You can do a search to find all the reasons you shouldn't save as a jpg so I won't bore you with that here.
And to recap, I now have a layout saved with the .psd format and an additional one with the .tif format. I save them in separate folders. Personal preference there.
But then what about naming them? Each of us has our own way to saving files to our compters and what works well for your other programs will probably work just fine here. I personally like to start the name of my layout with the date: 20100103, then with a one or two word description: 20100103 Ballet. Works well until you have more than one layout for a day. Then the additional problem if you have several that are related and one or two that are not. Below is an example of how I name my layout files. I like to make sure they fall in a certain order and this helps me out. Maybe it will help you too.
This is just how I do it. It is not carved in stone that you have to do it the same way. Find what is easiest for you and stick with it.