When you save a file in TurboTax, it overwrites the previous version. If you want to save multiple versions, you have to use the "Save as" or "Save a copy" command and give the file a different name.
The file with the ~ in front of the name is a temporary file created by the operating system when the main file is opened. It should automatically be deleted when you quit the program. If you have old files with ~ in their name, they can be deleted.
