To the OP: I went through the exact process starting about a year ago. I had been conservative-minded RC convert from a liberal secular upbringing for about 8-9 years, and my wife is cradle Orthodox (from Russia). She began to take her faith seriously a few years before our marriage, around when I was confirmed a Catholic. For a whle, we basically went the "two lungs" route, and accepted that there was truth in each of our churches, but after we got married, and had our first 2 children (#3 is coming, pray for us!), our desire for unity grew. We realized that it was nearly untenable for a family that wants to put God first to bounce from church to church, and if we were committed Christians who believed in the Apostolic Church, the True Church, "two lungs" just wouldn't cut it. We had some long talks, and mutually agreed to look into both faiths. I assumed that she would eventually convert, as I thought her allegiance to Orthodoxy was based in her Russian-ness, and I was so convinced of my own Catholicism.
At the end, we each had our own ways of searching. For her, she did some reading, but mostly praying, and she spoke with priests on both sides of the issue, including my former RC priest. I believe she had a lot of questions pop up, but that she never really felt strayed from the EOC. I, on the other hand, had a spiritual crisis, wavered so much that I avoided church for a month or two, and then eventually stopped trying to do so much darned research, attended services more, and met a good Orthodox priest. Once I/we stopped pushing,the Spirit, I believe, gently led us both into harmony in Orthodoxy. I will be chrismated soon.
I think my point is that the best things for us were A) to try to work things out in our own respective ways, B) not to push the issue too hard, i.e., don't go ahead and get em all baptized RC when no one's sure yet, and C) seek guidance in the Clergy and in Liturgy/mass! This is my two cents, and may the Lord have mercy on your family and bring you out of this time of confusion and into His church!