"De facto" is a legal way of saying, "It is what it is." When de facto refers to divorce, it is the arrangement that's in place at the time parents file, before any court order yet exists to establish custody terms or visitation. The de facto parent is the one the children live with if the other parent moves out of the marital home. She has unofficial physical custody because the children still reside with her.
If your divorce is bitter, it is possible that your spouse could refuse to let you see your children if you move out. She has all the power because she has de facto custody. The children are in her care and control, and you don't have a court order yet that you can enforce. You're effectively at her mercy, and typically, your only option is to file a motion right after you file for divorce or simultaneously with your divorce petition to rectify the situation. You can ask the court to issue a temporary custody order to control the situation until your divorce is final.
De facto custody can set a precedent for future custody proceedings in your divorce, so don't be surprised if your attorney advises against you moving out. Most courts will award temporary custody to the de facto parent if she remains in the family home; they're not going to make the children move out of their home, particularly early on in the divorce proceedings. An order can set visitation terms for you, but this places you in the position of being the "visiting" parent early in the proceedings. A temporary custody order can turn into permanent custody provisions in your decree for the same reason – the court wants to maintain the status quo. If your children have been doing well with your spouse, first when she was their de facto custodian and then under the terms of the temporary order, a judge might be reluctant to remove them from her primary care because there is really no reason to do so.
Best Interests of the Child
The bottom line with a court's custody decision is always the best interests of the children. Courts in many states look to which parent was their primary caregiver when the family was intact; if this is the same parent who had de facto custody and temporary custody, this creates another hurdle for the other parent to overcome. Some states, such as Maryland, will also consider "abandonment of custody" as a best interests factor, particularly if your marriage has been troubled for some time and you have a history of moving out only to come home again, and if you left your spouse with de facto custody of your children each time.
De facto custody can include other relationships beyond parent and child. For example, if something extraordinary should occur and neither you nor your spouse could care for your children for a period of time, the individual they live with while you're unavailable or incapable can become their de facto custodian. This might be a grandparent or a close family friend. Although this doesn't set the same precedent regarding future custody proceedings, the third party might still be able to petition the court for visitation as part of your divorce case. Parents are preferred for custody unless they are unfit, so it is unlikely that a court would place your children with a third party over either you or your spouse. Additionally, the court must first declare the third party as a bona fide de facto custodian, and this requires that certain criteria must be met. For example, in South Carolina, the individual must have lived with and supported your child for at least six months or sometimes even longer, depending on her age.