You'll add the jalapeños and cheddar during the fourth and final stretch-and-fold.
This is an important little step: make sure your jalapeños are very dry before adding them to the dough.
Drain the pickled jalapeños and pat them thoroughly dry with paper towels. You want to remove as much excess moisture as possible.
For the final stretch-and-fold, add some of the cheese and jalapeños as you work your way around the dough. Don't worry if they aren't perfectly distributed at first.
As you shape and fold the dough, gently press the additions into the dough with your fingers so they become incorporated without tearing the dough.