What I do in the winter for my buns, is stuff the bedroom area of the hutch with straw. Literally, I really pack it in! They love it haha
You can also get heatpads which can be placed in the cage under the straw and substrate.
I have my hutches covered over during the worst weather. During the day they have clear plastic sheet (like tarpaulin) so they can see out, but the rain and wind can't get in, and at night they have blue tarpaulin sheet covered over the plastic sheet to make sure they don't get cold!
Maybe just have one door of the cage open?
Do you have a photo of your setup? I could help if I can see how its all laid out