Question
When a word ends which is Mushad-dad when you come to at the end of an ayaah, how will that last letter of that word will be read? With sukoon or Fathaa. (e.g. Raa Mushaddad)

Answer
Arabs always stop with sukoon, so a letter with a shaddah on it is read with a sukoon when stopping.  There is however an accent we apply when stopping on a word with a shaddah, for most letters, to make clear that there are two letters present, meaning the two letters of the shaddah. 
Please see for the details and examples:
http://www.abouttajweed.com/the-accent-in-recitation-of-the-glorious-qur-an/the-accent-in-recitation-of-the-glorious-quran-p-2.html