If you are planning on doing deep bedding in the run, then I would suggest a layer of sand and soil over the run before you put down rice hulls. If you are just planning on mucking out the rice hulls every few days, then I wouldn't bother with sand.
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Would love to see photos of your new keets 
So far, the bedding is so deep that when we get heavy rain, we don't get any run-off. The organic matter absorbs all the rain. The bedding will be soggy for a few days, but they quickly turn it over and dry it out. Anywhere we dig out there, there are TONS of worms. My Thai mama hen spends ALL DAY digging up worms for her babies. The babies are super healthy and hardly eat any corn and rice. Sometimes they don't even come when I throw it down, they're too busy with worms!
We take large amounts of the bedding out on an almost weekly basis, and replace it wish fresh rice hulls. The "used up" rice hulls are mixed into our garden beds and used for mulch. So far it seems like a win win situation. . . . . But we haven't been through the really rainy season yet so we shall see how that works out. So far though, so good. All of the birds out there are extremely healthy and vigorous.
Thank you! I think that's what I'll do, at least in the short term. I can separate my Brahmas and RIR into the two outside sections, and maybe put a couple of guinea fowl in the middle section (with a large dog size door in one adjoining wall, which can be closed as necessary). Perhaps this will give me some time to see how well the guineas get along with the chickens (particularly my roosters) and if all goes well I might then take down the adjoining wall more fully. 