I have been thinking more about the confusion that you expressed and have to assure that is part of the process. There are so many ways to order a truck that every dealer I talked to was as lost as you are. I guess that I enjoyed the challenge and literally spent hours comparing packages and trim levels and separate options before I finally settled on what I wanted. In my experience every dealer pretty much just replaces what is selling well without putting much thought into it and just a little variation.
I did notice that as I built a truck on the Ford site that the address bar at the top contains all of the build information and that you can save several to make comparing different approaches easier. Now for the real "What the heck?!" moment. After settling on what I wanted I thought that I had stumbled on an easy way to communicate it to the dealer. I just copied the address bar at the top of the page and emailed it to my dealer. It turns out that the dealer ordering systems has absolutely nothing in common with the "build it yourself" system. Neither the option numbers nor the option descriptions matched between the systems. I had to print off what I had built on the customer site and spend at least 30 minutes with the dealer helping him figure out what that translated to on his ordering system. Some was guess work and sometimes we just had to match things according to list price. It was absolutely rediculous! Nevertheless, I would not want to commit to spending that much money any other way.