It's only abandonment if you leave the house and basically are never heard from again. You will need to find your own place to live as well as continue to pay for the old house. When you move out, take anything of personal value to you. Ex-spouses can get bitter quick and before you know your old family albums will be in the dumpster if you don't get them first. Also get copies or originals of any important documents... kids birth certificates, ss cards, bank statements, deeds, etc.
To be perfectly honest, you are at a HUGE disadvantage. Because she doesn't' work, that makes her the dependent spouse. Unless she committed adultery then you will owe her post-separation support, alimony and child support. The mortgage of the house (that she continues to live in) will be a dominant factor in establishing alimony.
Moving out will not affect custody. Keep well documented records of everything you do for the kids (doctor's appointments, homework, field trips). This will help bolster your claim if you want more than 50/50 custody. Do not take less time than you want, it's very hard to get it back later. If you can successfully prove that she is incapable of taking care of the girls then you may get full custody (be prepared to show proof).
If you can afford an attorney I would highly recommend one, and consult with them prior to doing anything.