We always just parked at the trailhead on the Trans America. None our "hikes" were more than a few miles though.
I have considered combining backpacking and bike touring and decided to keep the two separate.
A lot of folks say they leave their bikes in town, at a KOA, or with a business. I am a bit puzzled by that since where I have backpacked the trail heads are never near towns and seldom near campgrounds. Anyone care to elaborate on how they pull that off?