Hello from a complete newbie!

I guess I'm one of those people who makes the people in the know sigh a little bit.
We are the proud new owners of three little girls...

Pepper is a Barred Rock,
I'm guessing she's about 4+ weeks old.
And:

Chocolate, a Black Star, and Cinnamon, a Red Star.

We brought them home from the feed store yesterday and set them up in separate "brooding pens;" two big 40gal totes. Pepper immediately taught us how little we know (or how much we've forgotten!) about raising chickens by jumping right out of her pen and, after a few minutes of exploration, jumping in with the little ones. I was horrified! She'd peck the little ones! Nope, little Chocolate first pecked her in the eye, then on the comb! So Pepper got put back into her pen, now with a lid. Since then, until I caved this morning, she spent all her time trying to get back in with the little ones, not eating and trashing her pen. And she had all night to do it by the light of the little ones' heat light. Fortunately, this morning, everyone is getting along like gangbusters, except that Pepper has a bloody spot on her comb that looks like a rip (which I think is the result of whacking her head on the top of her cage overnight rather than a peck.)

So, is it true that chickens will continue to peck at a red spot until real damage is done? The terrible two seem to be leaving her alone now, but I remember from my Poultry Nutrition classes (I've a B.Sc. in Nutritional Sciences) that one of the reasons for clipping chicken's beaks was to prevent this kind of behaviour (yes, that was a very long time ago!)

They've already demonstrated strong personalities, I think Chocolate (who is the youngest and smallest right now) will be the dominant, Cinnamon is very curious, as long as she has her partner in crime and Pepper wants up whenever she spots a people! Who knew?

So, let's see...
We bought backyard chickens because we want eggs and like to watch our neighbour's chickens.
We are in Orlando, Florida, so the girls are 100% illegal (shhhh...) but many of our neighbours have poultry and I figure if the guy with the rooster who crows at any time of day or night or the neighbour with 25+ ducks haven't had a problem, we should be fine.

Now we have to get cracking building a nice secure coop and run for them outside in the garden!

I'm wondering whether we need to provide a substrate in addition to the native soil? We're building the run on top of a raised garden bed that just didn't work due to root incursions and not enough light. I figure that the sandy soil will be sufficient, but my husband thinks we should add something else like landscaping mulch, straw (or hay) or gravel.