Finally got it to connect by flashing to Universal then back to vehicle specific.
My current configuration is sub in stock enclosure, 6.5 mid bass in rear doors, 6x9 threeway in front doors, and tweeters. Currently I do not have the tweeters wired in to my amp since its a 5 channel amp.
What output configuration should I use on the app?
First things first, running three way in the door and tweeters in the pillars destroys your sound stage. You create a wall of sound vs an image on the dash. You need components upfront with a crossover. The doors are already a terrible location for speakers to begin with. By adding three way in the door, you make it worse.
Second, The DSR1 is designed to replace the factory Sony amp/dsp completely. That factory amp is what powers the tweeters in the pillars so I would be interested to see how you are able to get those to play.
Your setup should look like this:
You really need to replace those door speakers with a real set of components. Install the crossovers at the rear of the truck at your amp output. The output from the crossovers will run into the factory speaker harness provided in FO2 harness kit.