Would it cause to many conflicts in marriage?
How would you marry? Would you lie to marry through the church? How would you rise your children? I want them to not participate in church activities till they know why they are praying and to give them a fair chance to see what they really wont. What do you think? She already knows this and she agrees and disagrees with some. What do you think?
No. Do not get married until you both are in agreement.
It will only cause conflict, especially when you have children.
It sounds like you've already thought some of that through, but not through enough. If you don't raise them in the church, how are they going to know about prayer and the things of church? If you leave kids to make up their own minds, do you know what they'll choose? Nothing.
Or they'll choose what their friends are doing, which could be worse.
Or they could listen to some fanatical leader of a group that drinks poisoned cool aid because their leader was leading them to paradise. Even though one of you is an atheist, I will still lean on the only authority I know to be true...and always has been true...
The Bible. It says to not be unequally yoked with unbelievers. Think of two horses, pulling a wagon together. If one of them wants to go get a drink and the other doesn't, that's going to cause a conflict. Who wins? Usually, it's the one who has a weak faith in God.
They usually give in because they would rather have peace than try to prove something they're not really firm with, and they don't completely understand themselves.
I know the Catholic church will not marry you unless you both convert to being Catholics AND promise to raise your kids in the Catholic church.
If you lie to the church, what does that say about your faith? And who are you really fooling? You think God doesn't know what you're up to? You think He would be shocked to know you're thinking of such things? This union will never work out because you have divided loyalties.
And one of you are already caving in, being willing to let your kids "discover" their own beliefs.
Why not let them discover everything they want for themselves?
Why get in their way when they discover that Satanism or the Hell's Angels or being a gang banger is their "belief system"? You HAVE to set the examples for them to follow.
If you don't set the example, who WILL they follow? You see where I'm going here? I don't mean to sound holier than thou or demeaning your choices. But this is very serious.
You're laying the foundation for your family. What do you want to build it on... shifting sands of indecision (or no decision)... or on the rock that will not be shaken even when the bad times come... and come they will. If you are not both sold out on the same beliefs, your kids will suffer... and your relationship will suffer.
For your sake, and your childrens', take the high road and choose Jesus all the way.