Congrats hookem!! You should have lots-o-fun with a new jon.
I'm sure you will get many suggestions, I just had a quick thought to throw by you. I have a 12'er that I throw into the back of my Tacoma every so often, and it is great for many reasons. #1, cheaper on gas to have it it the bed rather than a trailer (slightly), #2, you can access more lakes without having to have a boat launch. #3 no worries about trailer issues (bearing, lights, ect.)
With all that said, having a trailer available is mighty handy IMO. I know you said two people, so that makes loading and unloading easier. But I found, If I go fishing like two or three times a week, it kinda becomes a pain to unload all your gear (motor also if you are looking at an outboard) in and out of the truck three times a week. You can definitely do it, and I still do depending on the lake I choose to fish, but more and more often I find it easier just to keep it on a trailer, ready to go on a moments notice. Just a thought. I guess you just have to evaluate your particular situation/needs.
The only other thing, (which is extremely basic) the measurements on the truck. You probably have about a 44"-48" or so working width and maybe 6' length in the Explorer??? Overall, on top might be a pain. I used to put the 12'er on top of my corolla wagon, but it takes more time and planning......But the looks you get are priceless!!!
Best of luck...
I have caught many fish in my life. The most exciting? The next one.....