I have this problem as well... I only let Lucky free roam in one room, and it is the same room that my dog hangs out the most in, so her food is there too... but then Lucky started to get in to her kibble. So I raised it up off the floor... but then he just started jumping up and getting in to it again. I can't raise it up much higher because Ginger is a small dog (italian greyhound), and if it gets raised up much higher, there is no way she can reach it. For now, I've had to move it out of the room... but I don't really like that option because I'm worried that Ginger will not get enough kibble if it's out of the room. My work around at the moment is to get a small bowl of kibbles and keep it on a bookshelf. When Lucky takes his late morning / early afternoon nap, put him in the cage and set the food down on the ground for Ginger. That way it's on the floor for her for a couple of hours for her to graze on. She also has a chance to eat kibbles when I leave the house, because Lucky goes in his cage at that time and she has free access to the kibble in the hall.
I don't really like this solution and I'm trying to figure out something better to do, but I'm just not sure what that is yet...