I’m calling the closed-in part the coop and the fenced in part the run. I’m not sure we are talking about the same thing. I’d keep them locked in the closed-in coop part for a few weeks.
I don’t know how high that closed in part is off the ground, but a ladder, ramp, or even an intermediate step will work. I’ve seen two week old chicks fly vertically up and three feet horizontal without a problem. It was obvious watching them that they could go a lot further if they wanted to.
The first few nights after you let them into the run section, they may decide to sleep at the foot of that ladder instead of going into the coop section. Mine do that a lot the first few nights. I just go down there at dark and toss them inside. Some catch on immediately but some occasionally take a week or even two to figure out they are supposed to go inside to sleep.