I prefer to put my bike(s) in the back. I fold down the left side, remove the front wheel, and lean the bike over on the edge of the upright right side.
I have a 56cm lightweight road bike, so if you have one taller, you may have to lean it more, fold down both sides, or take off both wheels. A mountain bike may be tougher to stuff in there, but someone on this site has done it. If you don't have a spare tire, you can lower the cargo floor for a couple extra inches clearance.
I also purchased a set of cross-bars (Wispbar from Yakima) and a roof-top bike carrier, but I haven't had the need to use it yet. I have a plastic folding step stool to make it easier to get the bike on and off the roof when I use the bike carrier.