I would start and kind of end with MK. If you're going to be there 12 days, you can easily stick MK somewhere in the middle too, if just to walk through to a meal or something.
In most of the guide books they say to start with the other parks and end with MK because the kids will be disappointed with the other parks. I don't agree that you should leave the "best for last". I think that's the park they're excited to see at that age and it should be first. Spend the first day there, take a break and go somewhere else for the night. Do the night time parade and wishes later in the week. Stick in a meal at the castle or one of the resturants at MK.
When I was planning my vacation for my neice 7 and nephew 11, I wanted to start in MK and end with lunch at the castle. It didn't end up that way, just because we couldn't fit something like that on our last day. We started with MK, EMH, then 10:00 reservations at CRT. It was wonderful. We had a wonderful ending to the trip also. ~~~ the Lion King and pizza at Pizzafari, turned out perfect!!!