I put the rain cover on my backpack. Usually, when I'm traveling I have just a small Lowepro Flipside Sport 10L AW backpack to fit my gear and if the rain becomes more serious, I put my backpack in front of me and cover it also with my coat.
For the camera and lens I always have in my backpack a water protection bag that will cover my gear so I can keep shooting in the rain if I need to. I tend to protect my gear and not relly on "weather resistant" thing.
If I go from cold to hot temperatures, before I enter in the warm place (my home for example) I take out the memory card and I let the camera in the backpack until it will reach the temperature inside my home. Why I take out my memory card? Because I want to look at picture without waiting a few hours for my gear to reach the temperature inside my home.