Smoke, having key fobs that will unlock and not do anything else is a fairly common issue, I believe, and is often solved by reprogramming the fobs to the truck. A tedious, but doable procedure that is well documented on this site. However, before you do it, you certainly want to make sure the functions will work from the switches inside the truck. And you might also want to test your fobs. Most auto parts stores have a little tester where you just push the buttons on your remotes and if they are broadcasting a signal, the tester will light up. If your switches work and the fobs test out okay, then reprogramming may get your fobs operational again. Most people that try the programming procedure find they have to do it several times before it works. It's a timing thing and you basically get it once you are able to memorize it and not have to stop and read each step from a piece of paper.
When I first got my runner, 1 fob would only unlock the doors and would do nothing else. The other fob wouldn't do anything. Replaced batteries in both and still the same. Found and followed the reprogramming procedure and on about the third or fourth try, I got both fobs programmed and they both function fully now.