Erasmus is a very good place to start, especially his work on the Praise of Folly. He employs a lot of classical allusions in that piece, as well as some allusions to the comedia del arte that was popular in the Italian middle ages and Renaissance. The mixing of those two tends also leads one to think of the passion plays that were also popular at that time. So, Erasmus definitely relies on both the Bible and the mythological tradition in his writing, using it to defend the Church.
I would also look at Montaigne's Essays. Although he leans more heavily on Classical models, he also combines Biblical and Classical references. He is interesting because his education was almost entirely humanistic, with little influence of the Church, which was rare at that time in France. So, he is at one extreme of the spectrum.
Another author is Thomas More and his Utopia. Many of the practices of the Utopian society can be seen in the Spartans of Greece. Again, his allusions are mainly Classical, but the story is being retold by Raphael Hythloday, so there are overtones of Christianity in his work. However, the Utopian society's religion, or lack thereof, is certainly far from Christianity. Although More's work is more Classical than Christian, More himself was a devout defender of the faith.
I would also look at some of the art at the time. Michelangelo's paintings of the Sistine Chapel are very interesting since they combine Classical and Biblical allusions simultaneously. He paints Sibyls next to Biblical prophets on the pendants of the ceiling. Moreover, Michelangelo paints many of his figures like Greek and Roman gods and goddesses in ancient statues. Also in the Vatican is a famous painting of the School of Athens by Raphael. Here there are no Biblical references, only pagan philosophers engaged in teaching and learning. Interesting that this painting appears in a chapel in the Vatican where Christian theologians were teaching, learning, studying and influencing Christian doctrine.
This topic is complex since there are no cut or dry answers. These artists and authors were mainly devout Christians who had studied the Classics and appreciated the ancient ideas. They also realized that art and literature have languages all their own. Much of that artistic language uses pagan symbols to convey ideas, even if they are Christian ideas.
Offhand I cannot think of anyone who is an authority on that subject, but a good place to start would actually be C.S. Lewis. His scholarly works cover the time period that you are talking about and he himself was a Christian dealing with the pagan tradition. I know that Bruce Young in the English department has done a lot of work on C.S. Lewis and Christian themes in English literature in general. I would contact him as well.
And a second email a little bit later...
I just looked at my copy of the Praise of Folly, and I found some authors who are experts on humanism during that time period. I would research the writings of Robert M. Adams as well as Paul Oskar Kristeller. Mikhail Bakhtin may also have some research on your topic as well.
Hope that helps!
Not all of this will work into my paper as I'm focusing on Milton but having ideas and examples from other people will definitely help to back my argument!