Hi, and welcome to BYC!
Good luck with all your plans. 


Follow along with the video below to see how to install our site as a web app on your home screen.
Note: This feature may not be available in some browsers.
I agree with the soil option and the earlier sand recommendation, as you know they will dig.Welcome back to chickens.
Dirt...I like peat moss.
Put a deep layer of dirt over the 1/2" hardware cloth. You are going to want EVERYTHING covered with 1/2" hardware cloth to keep predators out. Only covering the bottom foot isn't going to keep predators out.
If you rent and can't remove the stones you want to put the run over, how will you get rid of the massive amounts of poop that will be deposited on the stones and settle into them? Stones are not a good substrate for a chicken run.I rent and can’t remove the rocks and that’s the only place where I can put them so I don’t disturb his property. I am in casing the entire run. Thank you.
I would recommend a lip anyway to help keep out the bad guysSecond the no on peat moss - it can harbor very dangerous toxic organisms and make you and your chicks very sick. If you put a lip on your hoop run you can use sand bedding in it, otherwise wood chips will have the best chance of staying put.
Has he agreed to chickens yet? You better get it in writing so he doesn't change his mind (if he agreed) and evict you.I rent and can’t remove the rocks and that’s the only place where I can put them so I don’t disturb his property. I am in casing the entire run. Thank you.