Mike's info on shipping is on the money. Larger yachts are carried in "open-top" containers which are really open all around, with canvas covering sides and top. Larger yet are carried in open tops, but require special stowage to allow for dimensions beyond the container. You'll pay for that special stowage. Yachts shipped in the latter manner should be covered (shrink-wrap,etc..), although usually are not, resulting in stack gas debri which is very acidic depositing on them.
Your car will fit in a 20', although these are becoming rarer. Some companies will charge the same for a forty as for a twenty as it simplifies the stow. Generally speaking, your container would be carried within the stow and not on top with those spaces generally reserved for MTs.
As Mike indicated, the securing of your boat and goods internally is very important. This container may be going through thirty degree rolls as well as pitching back and forth. Do not worry too much about loss or damage. That is one of the principal advantages to containerization. If the cargo is properly secured inside the container you'll have a good out turn. Containers tend to go over the side in bunches, ie... the hatch cover is carried away. It is not a common occurence. In twenty years, I was never on a ship that lost one. If you have a stowage preference I would ask for inboard as, on the smaller feeder vessels, if a boarding sea is taken it can peel the side of the container right open.
APL serves Guam via the west coast and the Orient with feeders running into Guam a couple times a week. You can ship from anywhere in the US. APL will supply a sea container and then ship by truck/rail to San Pedro, Oakland, or Seattle. I believe the feeder service to Guam comes out of Naha, Okinawa.
As far as tainting damage referred to above, I think this to be a bit of a fish story. Years ago, in the break-bulk trade, we had to stow so that the tea from Ceylon was not stowed next to the jute from Cochin. You either got a pleasant smelling carpet or, more likely, disgusting smelling tea. Another advantage to containerization; we can ship taintable cargo adjacent to odiferous cargo with no mingling of odor.
If you're going to Guam, make sure you get up to Saipan, seventy-five miles north. If you don't scuba, take lessons, as they are inexpensive and the diving is some of the finest in the world-better than Hawaii. Ask for Ben in Saipan, he's Chamorran, everybody knows him, and he's an excellent dive master.