Sorry if this is a stupid question, but how exactly does one plan a long distance bike tour?

My dog and I hiked about half the Appalachian Trail last summer and I want to get out there and finish it. Instead of starting at the beginning or getting a ride to where we left off I decided it might be more fun to ride my bike from my front door in Tampa, FL to Waynesboro, VA at which point I'll be joining the rest of the AT hikers on my trip north to Katahdin, ME.

So, I have my origin, my destination, and a bunch of points of interest(mostly along the AT) I'd like to hit up figured out. I don't mind help but I don't want someone else to plan it for me; I want to know how you would normally figure out a route for something like this. How do you avoid bad roads and busy highways? What about steep inclines, unfriendly towns, etc?

Thanks,
Nick
instagram.com/nickandbruce