the "~" extra TurboTax file being generated

Those are autosaved copies of your .tax2018 file. One is created each time you start the program, and if I recall, about every 10 minutes or so while the program is open and being used. They come in handy if you really screw up and want to "back up" a bit. All you do is delete the current .tax2018 file and remove the tilde from the filename of the one you want to use. Of course, close the TTX program before doing that, and when you open it again it will use the tax file you removed the tilde from.

It's also okay to delete those that start with a tilde. But I suggest you keep at least the last one created. Murphy's law says if you don't keep it, then something will happen making you wish you had.