As long as your vet is willing to work with you and learn, you won't have a problem dealing with the fanconi. Just go to them and explain your test results, that genetically he has fanconi, but you don't know when (or possibly if) the disease will start to take effect. Bring a copy of the Protocol to your vet and ask them to read it and keep on file. They will usually do some digging to learn more about the disease at that point. But really it is very easy to diagnose and treat from the vet's standpoint. The hard part is how the dog responds to treatment and how well he'll take his meds.
The Protocol explains step by step what tests need to be run to diagnose the disease, and then what tests need to be done to determine the dosage of meds. It has clear charts and descriptions of how to interpret the results, so your vet can advise you on what to give. Also the biggest help is that Dr. Gonto is wonderful about working with owners and vets, so anytime you have questions you can contact him and he will work with you. When your vet starts you on treatment they can contact each other to make sure you guys are interpreting the Protocol correctly.
The only thing you really need to worry about now is making sure you find a place where you can use the blood gas machine for calculating bicarb dosage. Most regular vet clinics don't have this machine, usually just emergency vets, and it can be expensive to use. Also if you don't know a vet clinic in the area, most human hospitals have one. Ask around to see who will let you bring in dog's blood to use it. The test needs to be run very quickly after blood is drawn, so you might need to get the blood drawn at the vet with the machine or the nearest one to the human hospital. But your regular vet can do the other stuff.
Other than that, it's just sit and wait. You'll need to test the urine for several days in a row each month, and the more often the better. As soon as you start seeing the strip change colors, then it's off to the vet for the workups. The main strip test brand here is Bayer, they sell something called Diastix. You can order them online, but I'm not sure how bad shipping would be to you. I don't know what other brands are out there, but I would think you could find something at a local pharmacy. They are glucose urine test strips, do not get the strips that check ketones.
I'm very sorry to hear about Trouper's results, I hope that he doesn't develop anything for a long time! How old is Trouper? Usually the disease starts around ages 4-7, but sometimes not until their teens.