Since you're running a JB4 it's a little easier than the Cobb AP I'm using, depending on the mix you chose you might need to adjust the fuel pressure settings in the firmware; or eventually get the backend fueling flash that they offer. But off the bat you should be fine as-is just by running map 5.
It's a piece of cake, no real upkeep besides making sure you're running the right mix for the fueling scalar set in the tune. Easy way to do that is use the trip meter vs mile left in tank, assuming you reset the trip meter each time you fill up; add the two together, then divide the trip meter mileage by the total. Multiply that result by the gallon mix you're running, i.e. 50/50 mix on our cars would be 7gal, and that will give you the amount of E85 you need to put in; After adding E85 just fill up the remainder like normal with 93 or whatever highest octane you have access to.
There shouldn't be any additional wires to run E85, this is all handled within the firmware on the JB4. Most likely those wires are either for the SLD or NLS.
On an otherwise stock car you'll see gains up until about a 50/50 mix. Beyond that we won't see any benefits as we hit the upper limits of the stock turbos. Personally I'm running the equivalent of a 64/36 mix of gas/E85 (5gal of E85 to 9gal of 93), been having really good results so far, been able to throw a bit more timing and boost at it but haven't found the upper limit for the mix yet. Only reason I'm running this mix level is because I carry a 5gal jug of E85 with me at all times in case I need to fill at a station that doesn't have E85 (most don't carry it around where I live)