Use a rod tube. You can slide the rod in there still rigged up.I just had a rod break in half when my buddy who was driving slammed on his brakes and the cooler slide into the rod...
I like to use a two piece rod tube. I just take the rod in half while it's strung up and slide it in.
My Forester easily fits a fully rigged and assembled 9.5' rods with the 40 for the 60/40 split rear seat down. As I'm planning to get a truck, I've been thinking about how I'll store and secure various types of gear. Storing and carrying rods is a big downside to a truck vs SUV IMO.