The best option for kids and 2 rooms is get a suite. The second room is always cheaper in a suite than two seperate rooms. It's a few minutes outside of town, but close enough so that driving into town isn't a big deal:
http://www.hilton.com/en/hi/hotels/i...tyhocn=SDXSEHH
or Best Western offers a nice villa
http://www.bestwesternsedona.com/accommodations.html