Probably won't work with 5.5 bed without removing the front wheel, or flipping it around where the tire hangs off the tail gate. I have a supercab and usually use the tie down method (like you would with a motorcycle). With the 6.5 bed, you only have a couple inches of room behind the tire. If your only transporting one bike, you can also put it on an angle.
Anyways, if you have the option to get the longer bed, I'd go for it. Those are hard to find where I live. Plus you'll be able to fit a lot of other items aside from bikes. Its amazing what that extra foot in length will do.