I pretty much have exactly what you want to do. I have 5 hens who live in a large predator safe run on my side yard. When I say predator safe, I mean it's covered over the top with welded wire and welded wire is buried around the perimeter so nothing can dig in.
I let them out into the big garden only when I can be out there with them. Which is more often in the summer than the winter. Usually for several hours on Saturday when I'm out gardening. And during the week I let them out in the evening for 15-60 minutes.
They can definitely do some damage with their digging. But not to the point of destroying the garden. They tend to leave things that are as big as them or bigger alone. So my roses are fine. So are the ferns, iris, hydrengeas, etc. Now small, tender plants are free game and they will peck at them. Especially, if you do a veggie garden. I have trouble keeping them away from parsley and other herbs.
They also like to dust bath in soft dirt and they can make some pretty big craters. To avoid this, I make really desirable dust bathing areas in their run by softening up the soil, adding sand and peat and a little DE to keep mites at bay.
But you can barricade things. Buy a roll of welded wire from the hardware store and make big rounds out of it and place them over the top of things you want them to stay away from. Super light and easy to move around the garden.
They will kick dirt all over your patio so try to deter them from scratching right at the patio edge. I've got a spray bottle on the patio and discourage them with that. And it's worked. They stay away from the patio. But they will poop on the patio when they come up to me to beg for treats.
So you have to adjust your expectations a bit. But you can't co-exist peacefully.