So, I managed to get the 6 digit pin in by using the the instructions for Other Tax Situations in my desktop app, but when I proceed to attempt to e-file the app requests my 5 digit pin and wants me to enter it or create one or I am not allowed to proceed. Do I just create a new 5 digit pin at this point or am I missing something?
Those are two completely different PIN's. The five digit one is a "self-selected" number that you make up for yourself. The six digit IP PIN is issued by the IRS.
If you have a 6 digit PIN issued to you by the IRS you need to enter it in order to e-file. Go to Federal>Other Tax Situations>Other Return Info>Identity Protection PIN and enter the six-digit PIN.
Your signature ID (also called a self-select PIN)