I have a Chevy HHR, which does not have a trunk either. Here's what I do:
Stop at the VA border, unload my pistol, and put the magazine in my rammo box (which has a small padlock). The firearm then goes into a portable safe which is cable-locked to a tie-down loop in the back cargo area of the HHR. The ammo box is back there too, but not secured to the vehicle. Neither are easily accessible to me or passengers, and both containers are locked.
The firearm safe is NOT required by MD law to be secured to the vehicle, but I use a cable-lock so if someone breaks into my vehicle, the can't just bolt with the safe and open at their leisure.
The firearm must be unloaded and secured in MD. Whether or not the ammo must be in a separate container is unclear, so I err on the side of paranoia to be safe. Magazines may be loaded. If you want a copy of the MD AG's letter on this issue (I keep one in my ammo box, right on top so the AG's logo is visible when you first open the box...) search this forum--it's been posted several times.
Besides, if an LEO in MD wants to search my vehicle so he can roughly mishandle my ammo, magazines and firearm, he's going to need a warrant and a locksmith, because both containers are locked, and I think I may have left my keys on my other keychain at my wife's condo in Columbia MD...