My wife is a JW and I am no longer one. We went through a couple stages with our kids.
1. We both were in and were raising them as regular dubs. Making them sit at meetings, playing witness card/board games at home, family study, family service..puke puke puke
2. I started fading and kids kept going with mom to all meetings, service and conventions. No more family study or family witness games. Very little spiritual discussion at home. Kids would spout typical Jehovah loves or hates this/that and always telling neighbor kids that God's name is Jehovah and they must all use it. Very embarrassing; probably even for a non-fading dub. I was quiet and didn't step in to counter the spiritual activities. I did rearrange my schedule, including taking a lower paying job to be home more specifically so I could develop a strong bond with the kids.
3. I developed a super strong bond with the kids by devoting my time and energy to them. My wife continued to devote most of her time and energy to the borg. Kids eventually felt (maybe saw) the difference and each stopped attending on their own at different times. A couple of the kids have even mentioned how cult-like the dubs are and they wish mom would exit. They're angry with the dubs for making mom so 'weird' and 'different from other moms'. I don't bad talk my wife, even regarding the dubs, but I do agree with the kids that the dubs are a cult.
I guess my only real advice is to do whatever you can to build a strong bond with your kids and make sure no matter what they come first. You and your wife will fight, argue, makeup and maybe even divorce one day (who knows) but you and the kids are forever. Teach them to think for themselves. I've said this before but I even let the kids buy one or two toys advertised on tv as the best thing ever (we discussed how we would feel if once it arrived it really wasn't as great as the commercial said it was)...the products stunk...the kids learned a lesson, I was out $50. From then on the kids always do research online before buying anything (this was from a fairly young age). They realize that there is no difference between researching a product and researching someone's opinion or teaching. They have become good thinkers.
I wasn't raised to show much emotion but it broke my heart and brought tears to my eyes when my oldest told me that they were all afraid that mom wouldn't love them anymore if they stopped going to meetings. I assured them mom would love them just as much and that no matter what we would be there for them. Honestly, my wife's cult personality doesn't have much use for the kids, but her real personality loves them like crazy - must cause a lot of cognitive dissonance.
Also, be prepared that everything, I mean everything, wrong that the kids do to be your fault because you're not bringing them up Jehovah's way. It's wrong thinking but the dub in your wife won't see it that way. You will have a lot of weight on your shoulders. I think it's your job to take it all on to protect your kids from feeling any of it.