Heat oven to 350 degrees F. Line an 8"x 8" square baking pan with foil and spray with cooking spray.
Combine 1 cup of the dark chocolate chips with the butter in a large saucepan over low heat. Stir until melted. Remove pan from heat and let cool slightly. Stir in the sugar, vanilla, and salt. Beat in eggs, one at a time. Finally, add the almond flour and mix well. Pour half of the batter (about 1 cup) into the prepared pan, spreading out evenly. Bake for 15 minutes.
Meanwhile, melt the caramels with the cream in a small saucepan over low heat, stirring often. When the bottom part of the brownies is done baking, pour the melted caramel mixture over top and spread out evenly. Sprinkle with the remaining dark chocolate chips and the chopped pecans. Drop the remaining brownie batter by tablespoon-fulls over top.
Return to oven and continue baking for 20 - 25 minutes, or until top brownie is puffed up and tests clean with a toothpick.
Notes
I have read that Kraft caramels are gluten-free, but I suggest you do your own research to see what will be safe for you.