I've done this ride. There is parking at the trailhead in Boston PA - this is actually where I would advise starting. There is a store right by the trailhead. Maybe the owner could check your vehicle for you.
Weather conditions can be all over the place. Generally September should be pleasant, but if rainy the C&O will get extremely muddy. Also it can get cold in the Laurel Highlands area.
When we did the ride, we rode our bikes directly to Reagan Airport and rented a minivan with a drop off at Pittsburgh Airport. Two bikes fit in easily, so a bike and a bob should be no problem. The cost was about $80. We saw several people using bobs on the trip.
Take in everything, it's a beautiful ride. Take time to walk through Harper's Ferry. Also visit Steve at his B &; B in Little Orleans and eat breakfast at the GI Day Room in Meyersdale PA.
I promise you that the ride will be an experience of a lifetime. If you want to see my blog on the ride it is www.iadcbiketrip.blogspot.com. Unfortunately the bike that I used for the ride was run over and destroyed on Monday by Ken Zvirman, owner of Jo-Mar Provisions Inc 42 18th Street Pittsburgh, when he experience an uncontrollable fit of road rage.