i use galvanized roofing panels (the rumply kind) over my pens. i started off using pvc panels, the plastic rumply things, but they need a lot of support so as not to sag. The metal ones are more durable and easier to work with.
It is best to use 1/2" hardware cloth all around your pen, and i have some like that. But, depending on your location and predator situation, that may not be absolutely needed. i have some pens that are made from chain link kennel panels. The biggest problem i have here are rats, and for some reason they want to burrow under and into the pens, even though they can easily walk through the chain link panels.
For integrating flocks, i use sections of 4' tall 1/2" hardware cloth. i just section off part of the pen so everyone can see each other for a week or two. If integrating younger and smaller chickens, i will keep them in flight cages set inside the larger pen. i have mainly bantams, so this works well for me.
On planning a run, the larger the better, as large as you have space for. i find the bigger space eliminates or lessens bickering amongst the flock. Anyhow, good luck, and you are very wise for seeking advice before getting your chickens. i've always gotten the chickens first, thinking i have plenty of time before they're grown to build a coop and pen. Then i'm scrambling, trying to put something together at the last minute.