Under recent additions to PRK law, you can't just have a gun in your trunk at all times. You can only have one in the car when specifically transporting it to a location where you can legally have it (i.e., range, gunstore, your buddy's house with his express permission, etc.). This is specifically designed to prevent people from carrying guns in their car all the time.
Of course, provided you have a story ahead of time (yes, officer, I'm just coming back from my buddy's house where he helped me fix the stock swivel...) it would be hard to enforce. Most people will get busted, though, because they don't know it's illegal.
As long as the ammo is in a seperate container, it's fine. Do not, say, have loaded mags in the pockets of an "assault case" that contains the rifle; keep them separate.
Note also that under PRK law, if you are carrying a gun AND carrying the ammo for it on your person, the gun is legally loaded, with all that implies.
-Troy