Does functionalism or conflict theory do a better job in discussing religion and the effects of religion today?
"do a better job" than what?
This is an opinion question. Your teacher wants YOUR opinion, not someone else's.
Read lots and take notes. Let us know what you decide.
http://www.google.com/search?q=functionalism&oq=functionalism&aqs=chrome..69i57j69i61j69i60.2535j0j7&sourceid=chrome&es_sm=119&ie=UTF-8
and
http://www.google.com/search?q=conflict+theory&oq=conflict+theory&aqs=chrome..69i57j69i61.3624j0j7&sourceid=chrome&es_sm=119&ie=UTF-8