Why is it when I save a file it appears twice but one has ~$ at the front?

Do you mean an Microsoft Office file?

If so, then the second file is a system file that programs like Word and Excel create. MS Office programs create a second file when you open/edit a word or Excel document, and they edit this second file instead of editing the original. Then when you save your file it overwrites the original file with this second file.

It's done to help prevent damage/corruption to your original file if your computer crashes while you are editing a document. It means that you only loose the changes that you made since you last saved, and not the entire file.

The one with the ~$ in front of it is your "active" copy, and is usually hidden by the file system. What this means is that you have an application, such as Word, working on that file. When you save, you'll actually save to the real file. The ~$ is just a mechanism that some programs use to prevent data loss in the event of a crash. (Have you ever accidentally turned off your computer and when you restarted Word the next time and a dialog box pops up asking if you want to recover your file? That's because the ~$ didn't get deleted, usually.)

it is because you are changing the template of the normal file so it saves a second one that looks transparent with ~$ as it is the new template for the file you have just saved