What you can do legally varies by state, so be sure to check local laws.
With my disclaimer out of the way, I'll address your actual question.
In my home state, Washington, if you have a concealed carry permit you can carry a loaded pistol in your car without having to unload it or store it locked up. I often use a bladetech paddle holster that fits securely to my seat belt that way my pistol was out of my waistband and in a cross draw position. I found that to be the most comfortable way for me to travel any length of time in my car. It was easy and cheap, I think the holster was $20.
Other than that, I've usually just kept my pistol in the center console or glove box if it wasn't staying on my person.