Thanks for the clarification. A) If you are going to be providing 50% of the care (or more) then there is no reason to feel guilty about taking her money. It's not as though you are going to be using it for yourself...it's for the kids. It's not about your wife and isn't punitive...it's solely about the kids. Keep that firmly in mind. They need their dad and they need to be provided for financially. If things change down the line, you can always change the financial arrangement, but for now do what's right and get child support.
It sounds like you set the precedence of caring for the kids. I wish you weren't at your sister's and instead had stayed at the house til all this was worked out, but that's water under the bridge. Once you get your own place and get this legal stuff rolling, you'll be able to show that you are entitled to the time.
V1olin, I'm going to be brutally honest. The odds of saving your marriage by any technique is not that great. You have to worry about protecting yourself and your kids and worry about this "lack of respect" after. She might respect you more for making this stand.
You cannot be lonely if you like the person you're alone with. Dr. Wayne Dyer
