I think I can contribute something to this. My husband is muslim and I am atheist-when we met, I was wavering between agnosticism and atheism, been brought up in a non-practising protestand family.
When our child was born, we could fortunately agree easily that she would not receive religious education and would be free to choose for herself when grown-up.
After a couple of years, my stepsons joined the family, both having been brought up in the muslim faith.
For some years, my husband insisted on them doing their prayers together. As they could not pray during school, it led to them having to spend increasing time after school praying, which clashed with sports and hobbies. Finally, he gave up on the praying-it just doesn't fit in with an active childhood (yieppee-thank you soccer, dance etc.).
At school, none of them received religious education. They studied ethics/moral education instead (facilitated in a Catholic primary school!!!).
Growing up, every now and then each one had their doubts, curious about God, Allah, saints and the rest of it. Each time I explained things to the best of my knowledge-how the bible and the Quaran were written, why some christians believe in saints and others do not, why muslims don't eat pork and the rest of it.
All the time, it was agreed that the boys, too, would have the freedom to decide once they are 18. Well, one reached that age and wanted to be recorded as "no religion" on the census, the two younger have continuously expressed the same wish. I would say they are all three agnostics verging on atheism.
At home, the only concession I make of respect to my husband is to serve no pork products (fine, as long as I can enjoy my rashers). On the other hand, he doesn't pray anymore and I would classify him agnostic.
So: The other parent has the right to teach the kids his/her faith. It is your right to present the other side of the story - science programs about the universe and evolution are brilliant, absolutely brilliant in this. In the end, your kids choose for themselves when they grow up.
Ps-most importantly, choose a good spouse/partner!