Pheonix is right. You need to file. Monday if possible. If you don't have an attorney or can't afford one, you can do it pro se until you get one (or whatever).
You need to legally establish your custody, regardless if she has been away for 100 years. She can say anything she wants when she gets to court (you hid them, beat her, absued her, PAS, whatever..it's very common), so do it now.
At the same time, set up supervised visitation with the kids. If really is in their best interest anyway and after you win physical custody (which you will as long as she doesnt use the abuse card) you can expand the visitation arrangement if the boys want that. Your kids are no longer at the age where they are going to be influeced by her much anyway.
It's extremely important to establish this stuff legally. Get off your a** and do it Daddy-O...
BTW, your kids will have a LOT of input into this as far as the court is concerned. Heck, one is going to be emancipated in a couple of years..it's not like they are infants.