I pretty much did things the way you’re planning on, Skald. My kids are 13 and 10 now (I’m so OLD!) and the oldest is an atheist. The youngest isn’t religious, but is kind of interested in spiritual stuff generally. She has a big imagination though, and she gets it all kind of muddled up with magic, which she really really wants to be real. She’s at that funny age where she knows she’s growing up and is resisting it, HARD, so she’s sort of into believing in fairies and stuff. It doesn’t worry me.
When they were smaller my mom wanted to take them to church. Her church is pretty liberal (Disciples of Christ) and she and I have a … difficult relationship, so I decided this was not a battle I felt like fighting. After all, I went to church and look at me! It was a smart move; when they got older they hated it and refused to go. I obviously wasn’t going to make them, and that was the end of it. Incidentally, my mother has left the faith now as well.
I have always strongly stressed morals and ethics, and tried to teach them how to logically deduce the best course of action in a given scenario. Rather than teach them rules like religion does, I try to give them the tools they need to make their own choices. If one day that choice is to be religious, I can’t say I won’t be a little baffled, but I’ll accept it. I really really doubt that will happen though.
Also, specific to your circumstances, living as an atheist in the south is hard, and it needs special instruction for kids, in my opinion. My kids understand that people will NOT accept their disbelief, and that they may lose friends over it. Obviously we don’t make fun of someone’s beliefs, that’s just basic manners, but I’ve stressed to them how very very upset people get over this topic. I’ve told them that it’s their decision how open they want to be about their (lack of) beliefs, and that I support them no matter what. Currently my oldest is pretty closeted about his atheism. In school situations when it gets muddled (he’s had teachers talking about Jesus in class for example, and yes this is a public school) I’ve told him that if he wants to stand up and try to change things, I will stand beside him 100% all the way, but that I cannot protect him from the fallout, which could be severe. So far he’s chosen to be silent, and I respect that.
Right now my only issue is with their dad (we’re divorced) because he started dating a Christian girl and now he’s trying to pretend he’s always been religious. Of course, my kids are kind of outing him. For example, he’ll mention how he goes to church, and they’ll say “no you don’t”. They’ve been with me all summer, so it’s at a simmer now, but I’m afraid it will get ugly when school starts soon and they are staying with him again. Ughhhh. But, that’s a separate issue I hope you never have to deal with, and I don’t want to go off on a tangent about what a stupid asshole he is. 
eta: there’s a REALLY great kids book by Dawkins called The Magic of Reality about science and history and evolution and religion. I bought it for my son a few years ago and he loved it. Your kid is probably too little now, but (despite his reputation) I found it deals with this stuff in a really good way. You might want to pick it up