You will purchase a programmer, then install it on your truck.
You will contact the tuner (I used Hemifever) and make the arrangements for a custom tune. They will have questions for you on what sort of modifications you have (intake, exhaust, tires/wheel sizes, etc....) and what, if any, specific tuning tweaks you want like what octane will you be running (I ran 92) whether or not you want MDS turned off (I specifically asked for that to be done) and anything else that you would like to address like WOT shift points, etc..
You will then log the truck's performance using the programmer. Then you'll download them to your PC and send your logs and last written tune via email to the tuner.
They will perform the tuning tweaks and send you a tune file via email. You'll load that tune file onto your programmer, then install it on the truck much like you did when you first programmed your vehicle. You'll log again, then send back the logs to the tuner for another tweak. I think I did this three times with Hemifever.
Note what hemi450hp said about the programmer warranty and cost of tunes. By the time you add it all up it may be cheaper to go with a new I3 programmer.
Also note what RedSTR4Me said about saving the tune files you are sent in the right place on the programmer when you get them.
You will get instructions on most of this with your custom program.