There are a couple of things to think about when you talk with a lawyer. First, my wife and I didn't have a separation agreement so I was able to prevent her from taking my sons when they didn't want to leave me because we weren't divorced and we had no agreement. That worked to my advantage. Second, and this is something I didn't know prior to mediation, I was supposed to be paying child support during separation. Of course, if you have your children 100% of the time, there's no reason to pay child support to your wife.
Given your circumstances, or given your wife's current lifestyle, I wonder if she really cares if she has custody of the children. I'm sure she'll say she wants custody, but if she's not being a good mom, then now may be a good opportunity to make a case against allowing a 50-50 custody agreement.