If mileage is your goal, go with a 5-speed. If reliability is your goal, go with a 5-speed. If you want to sacrifice those two in the name of not having to think about shifting, then go with an auto...and you might as well go with a gas engine. Just my opinion, and many will disagree. I have a Dodge Cummins with an auto, and its the worse piece of junk I could ever imagine. The torque doesn't make it to the ground...it just revs up and makes noise. Its also the 3rd transmission for this truck in the past 100k miles, I don't know how many before that...the records don't show. Its at 260k now. $4k+ per trans and install for 30k or so of use is pretty expensive. My Dakota went through 2 auto transmissions before I bought it, and number 3 went out at 80k. I had 2 Grand Cherokees, 4 transmissions between the 2 of them. All of those were with gas engines, and not the low RPM abuse a diesel gives an auto.
Other than an auto being a poor choice behind a diesel, welcome to this site and congrats for thinking about a Cummins!
Jim