It's possible to not adhere to someone else's beliefs without undermining those beliefs
This is a concept that took me some years into my adulthood to really understand. In my youth, I was fervently anti-theistic agnostic. Then I spent time as a very devoted member of an almost fundamentalist sect of Christianity. Now, I've comfortably settled into a comfortable ambivalent atheism. It's only been in this latter stage where I've realized how to disagree with someone else's beliefs without trying to tear them down.
Keeping a respectful, accepting tone when speaking of other belief systems is of tantamount importance. You don't want to be condescending, incredulous, or even skeptical in your tone. Likewise, when talking about your own beliefs you don't want to sound superior, cocky, or aggressive. Using non-neutral tones is divisive, and may actually make actually be counter-productive.
It's possible to participate in religious activities as an atheist without being a hypocrite
If people are praying, you can participate by being present and being silent while everyone else is doing the prayer. In this way, you're respecting their beliefs without disrespecting your own. If asked to pray, you can politely decline.
If your children need to study religious material, you can help them study it. What you're doing is spending quality time with your child that's also educational. Some schools teach about Greek myths (or other myths) or other religions (Judaism and Islam), but I doubt you'd feel hypocritical helping them study those materials.
Helping your child learn something that is important to them, and doesn't teach them values you find abhorrent, is something you should strive for regardless of the religiosity of the material. At this point in time, they may be putting what they're studying into practice, but you'll need to mentally separate helping your child learn and be successful from what they're learning and how they're being successful.
It's the responsibility of the parents to ensure their children are receiving well-rounded education
While you hope that the school will teach critical thinking skills, and maybe some level of skepticism, it's ultimately your responsibility to do that. If you want your children to be aware of other belief systems, including non-religions, then you'll have to teach about them. The best way to do this, of course, is by being educated about the different belief systems yourself.
When your children ask questions that may have a religious answer, you can answer with a variety of options. For example:
"What happens when we die?"
"Well, Catholics and some other religions believe you may go to Heaven. But, some religions think you may come back to Earth as someone else. And some people don't think anything happens at all."
Granted, these are simplified versions of complex beliefs on the matter, but they'd do well to answer a child's question and maybe inspire some curiosity.
It'd be up to you as to whether or not you'd wanted to introduce more structured teaching about other religions. Personally, I think answering applicable questions with two or more beliefs is an adequate way to handle this. Your child learns there are other beliefs, and can dig deeper into them if they desire. If you're presenting all alternatives with the same accepting tone, then your child will pick up on the fact that it's okay to have those other beliefs.
You should be honest with your children
At some point, I think it'll be best if you have a family meeting and explain mom's and dad's beliefs, and how they're different. There's no reason for your children to know only your wife's beliefs. If you're made to be uncomfortable sharing what you think, then the relationship is not equal.
The meeting could go something like this:
- Ask the children if they know how there's different types of Christianity besides Catholicism. Like Protestants or Baptists. If not, teach.
- Then ask if know that there's other religions besides Christianity. Like Judaism, Islam, or Hinduism. If not, teach.
- Then ask if they know that some people don't have any religion. Like Agnosticism or Atheism. If not, teach.
- Then talk to them about how Mom is Catholic, and Dad is Atheist (or Agnostic). Avoid the phrase "Mom is Catholic, but Dad is Atheist". Try to phrase it a way that is completely neutral
- Ask if they have any questions for you
- Let them know they can always ask you (both) questions about these things
- Assure them that even though Dad isn't Catholic, he'll still support them in their Catholic activities
- Assure them that even though Mom isn't Atheist, she'll still support them if they choose non-Catholic activities
- Assure them that if they ever want to learn about a religion that isn't Mom or Dad's, then you'll both support them
The parents need to be on the same page
You'll obviously need your wife's full support for this meeting to happen. She has to be willing to allow you to share your beliefs, but also agree to abide by the idea of supporting the children if they choose not to continue in Catholic beliefs in the future. Please note, I'm not talking about school. Children can get a fine education at a Catholic school without necessarily taking Catholicism to heart. There's no real reason that changing schools needs to even be discussed.
You also have to agree on the when of this meeting. It shouldn't be held off for any reason, but it's not immediately pressing. Ideally, your children would have reach their current ages already knowing this stuff. (Ideally to me, that is.) However, if you're worried this may affect your son's commitment to his First Communion, then it may be best to wait until after that. Not because that belief is more important than yours, but your son's mental health is more important than your beliefs.
Lastly, you'll have to agree to answer questions in a way that takes into account both parents. You'll need to try and answer the relevant questions the way your wife would and the way you would. She should also be trying to answer such questions for herself and for you. This way, you're presenting yourself to your children as a team that understands one another and works in unity, even if not together. If one of you isn't quite sure how to answer in a way the other parent would, then it'd be a great time to say, "I'm not sure what your [other parent] would say, so you should ask them."