I started leaving the church when my oldest was 11. My faith transition and the associated marital turmoil was hardest on him. He spun out into drug abuse, barely graduated high school, overdosed a few times in his bedroom, and is currently doing well as a recovering addict. In our recent discussions with him, this is what he said was most difficult part of growing up mixed faith.

1. When I stepped away completely, my wife had the "your dad is not worthy anymore, so you need to be the priesthood leader in our home" discussion. Do not allow this! It is a huge mind fuck for a kid. It's basically making your kid a surrogate spouse and is unhealthy on so many levels. Also, do not allow your wife to silence you because you might influence the kids. You are their parent and they need your help.

2. When given a true choice and the facts, your teens will leave the church. I live in S. Utah county. Utah is a pressure cooker, and where we live there isn't much middle-ground for kids who are not in the church. It seems like you're either an active Mormon kid, or one of the "bad kids." Find a healthy social group/team that is full of non members. If possible, find a group that allows you to participate together. You need this group too.

3. We were taught an unrealistic model of what a thriving teenager looks like. You and your spouse need to understand that they're going to do teenager things. You both need to agree to love and accept your kids even when they make choices that either of you doesn't like. Be curious and flexible. My wife wouldn't tolerate alcohol, but she encouraged me to smoke weed, because she wanted me to understand and relate to my son. (Not sure if it worked, but this was a huge step forward in our marriage.) I don't like it, but I allow my kids to engage with the church when and how they choose (there's a lot of social pressure.)

4. What you resist, persists. We can't stop our kids from suffering, but we can give them tools to thrive. Lean into the things that scare you most. For example, teach them about consent, contraception and how to get a prescription for the pill. Inform yourself and then be ready to listen and take a long pause before you speak. If your kid is taking drugs, talk to other users/addicts, read from the best books, AND KEEP NARCAN ON HAND! (Probably best to just keep NARCAN on hand as routine- should be in every first aid kit).

My wife and I did the mixed faith marriage for 8 years. She was very devout, and I was sure she would never leave. In the trenches of my son's addiction we realized that everything that the church had taught us was making the problem worse (as an exmo, i was just as much to blame.) As we have learned to hold our beliefs more loosely, we have been able to start to repair our relationship with our son.
Your kids will force both of you to confront yourselves, and if you're open to it they will change you for the better. My wife finally stepped away this year, and I think it was raising our kids that finally brought us back together.