Leaving the bikes in the car will do nothing to stop them getting pinched. Just means you end up being more annoyed when your bike has been stolen and someone has crow barred your car door open.
I have been there twice this week, most recently yesterday and there are a lot of notices now up telling people to leave nothing on show.
Aside from that its a great trail center. Guys @ Skyline Bikes are extremely helpful and will help out with any problems as soon as they can. Trails are always in good nick what ever the weather.
A lot of the Skyline trail was still closed yesterday so if you are looking for a long day ride the W2 would be better. Also as mentioned above the Skyline does have a lot of fireroad which is boring as hell if it's cloudy and there is no view.