First, make your dough. Combine 1 cup warm water with the yeast and 1 tablespoon granulated sugar in the bowl of your stand mixer and let sit for 10 minutes until it bubbles up and foams.
Then add in half the flour, brown sugar, salt, oil and remaining water to the mix. Mix on low with a dough hook for 5 minutes, adding flour until your dough forms. Then knead by hand for another 5 minutes until you have a smooth but dry-to-the-touch dough. If dough is a little sticky, add a little flour as necessary.
Divide the dough into 10-12 pieces, form into balls and cover lightly with plastic wrap. Allow bagels to rest for 30 minutes and puff up.
Meanwhile, mix together cream cheese, lox and chives in a medium bowl.
Take each bagel and flatter slightly. Place about 1-tablespoon of filling in the middle of the bagel and form dough to cover cream cheese and make a ball. Place the dough balls seam side down, an inch or two apart on parchment-lined baking sheets. Cover loosely with plastic wrap and let rest for another 15 minutes. Test bagels for the "float test" but seeing if one floats in a bowl of room temperature water. If it floats, yay! Cover and refrigerate overnight, or up to two days. If it doesn't float, let bagels rest in 10 minute increments until they do.
Now time to boil and bake! Boiling your bagels gives it that crunchy outside and soft inside. Take the bagels out of the refrigerator 30 minutes before baking. Preheat oven to 450 degrees F. Prepare a cooling rack. Bring a large, wide pot of water to a boil, add baking soda, and boil bagels 3-4 at a time for 30 seconds on each side. Sprinkle with everything bagel spice and let bagels dry on cooling rack. Then bake on parchment-lined cookie sheet for 15 minutes or until golden brown. Let cool slightly and eat!
Notes
You will also need to let the bagels ferment overnight.