"Should I only be be entering my portion of the RMD?"
Yes, only enter as the required amount only the portion that you were required to take.
"there is no way to indicate that it is not my IRA"
Depending on which version of TurboTax you are using, on one of the pages that follow the entry of the Form 1099-R details, TurboTax will provide a checkbox will ask an explicit question where you will indicate that the IRA is inherited.
