Protect myself - can she say I deserted her or something? As far as my children go, I plan on filing for joint custody, they would live with their mother and I will see them frequently. I do that now.
You can't get into trouble for desertion.
As for custody, you should be OK, but try to see them as much now as you would hope to see them in the future. The court likes to enforce the status quo. If you're seeing them one evening a month while the divorce is pending, there's a chance you will only be seeing them one evening a month after the divorce. Likewise, if you have them every other weekend and every Wednesday now, chances are that's what you'll be able to get for the future.
If the separation is amicable, it wouldn't hurt to write down what your expectations are with respect to custody and visitation and having both parents sign it. It's not necessary, nor is it actually binding, but it does indicate that the two of you are working together to make sure that the kids don't get short-changed. In particular, if your stbx were to try to get sole custody on the basis of you leaving the house and the kids, it would support your statement that you were in agreement on custody and visitation.
