CONTEXT
Hello, I'm an engineer with some introductory level studies in philosophy. I need help (or at least a sanity check) from this group in an argument about cherry picking. I'm having an argument with someone but we've stalled in a deadlock. The context is that I'm a holist (trust in science, believe in God) and my opponent is an atheist (trusts in science, believes...?). My opponent has no studies, nor interest in philosophy...he's said "I don't need philosophy".
MY GOAL
I do not want to sneak in theism in this forum, neither do I want to sneak in a negative image of atheism/atheists, neither am I asking for tips to win an argument. I want to know what is the right way to understand our deadlock. I don't care about who is eventually right or wrong (atheism or theism), but I want to learn to apply philosophy to detect fallacies. I hope I'm in a right place in stack exchange. I'm hoping to get answers from both atheist- and believer-philosophers (or students of philosophy) so that I could formulate an coherent opinion. I am not a troll, I have a genuine interest in philosophy.
SITUATION
The deadlock is following. We (myself and the atheist) have argued about a book (the title is irrelevant) created by a Ph.D. (name irrelevant). The problem is, says the atheist very strongly, that author happens to be relatively known christian which makes his work "worthless". He says: "Christian scholars think like this: there is God, then they look thru research papers and cherry pick whatever supports god's existence".
I'm saying back that: "It ain't necessarily so since we can't read those christian scientists' minds. Christian and atheistic scholars MIGHT both be cherry picking but we don't know if they are or not so it's better not to use this line of argumentation at all.". This far I can handle, I'm thinking I'm argumenting rationally...
But then my opponent says very strongly: "No! Atheist scientists do REAL science. They work differently, they look for data objectively and go where the data leads. That's how is should be." So basically he is asserting a functional difference between how christian and atheistic scientists work. Personally I think he's trying set me on an uneven playing field. I think he is committing a genetic fallacy, ie. dismissing some pieces of science because of their source.
My problem is, that he has repeated this argumentation so many times already (in previous argument) and so strongly that I'm not sure anymore who is right. My gut tells me that I'm right, that there should be no difference between atheistic and christian self-respecting scientists, regarding their work habits. I don't believe there is significant cherry picking going on in either direction.
CONCLUSION
So, that is the dilemma recapped as best I could, not having twisted the quotes in any which way. I'm hoping someone can make sense of this situation and give me some advice what to think of this deadlock.
I appreciate your help! Thanks!
EDIT
I forgot to mention that my opponent has not read the book he is attacking. He says he doesn't need to, because he "has been aware the author's work for some time" and because he has read an online review of the book.
CONCLUSION I accepted CortAmmon's answer, but honestly every answer and comment contained something valuable for me. Just to let you know what happened, is that a) I asked for proof of cherry picking, b) pointed out his fallacies (and named them), c) pointed out he hadn't read the book he was criticising and d) that at least 65% of Nobel laureates have been religious.
He didn't address any of [a-d] in his follow-up, he only claimed that I don't address his arguments. So I decided to walk away from the "debate".
I counted he made the ad hominem in five separate replies, of which three after I had pointed to and named the fallacy. This was a true lesson learned for me.