Yeah. Ok. This info isn’t particularily “secret”. But if you like your bagels flavored beyond plain, read on.
For stuff on top of your bagel: This applies to sesame seeds, poppy seeds, salt, caraway, sunflower seeds etc. Get a small shallow plate and put a generous amount of your topping on the plate. As you scoop the bagel out of the boiling water with your slotted spoon, slide the bagel top-side-down right on the topping. This should be all you need to do, the topping will generously stick. Gently pick the bagel up with your hand and place it on the sheet pan with the topping facing up.
For fruity flavors: For example: cinnamon raisin, blueberry, strawberry. This is shown in the picture up at the top. Take a portion of dough that you would like flavored. Sprinkle with a little bit of cinnamon for blueberry and strawberry and a little bit more for cinnamon raisin. Now just fold the dough several times and knead the fruit and cinnamon into the dough. Then just portion and roll into a bagel shape accordingly.
Really awesome Everythings: Here is what to put on your Everything bagel: kosher salt, caraway, poppy seeds, sesame seeds, garlic and roasted onion. Seems straight forward but I actually cook the onions and garlic before putting on top of the raw bagel. I find this makes it really authentic.
The garlic you can do on the stove top by heating about 1 T of olive oil for 3-4 cloves of minced garlic. Cook the garlic quickly at medium heat until it is just cooked and barely browned, should take less than 1 minute. Set aside.
The onions, I put my oven onto about 415 degrees. I dice my onions small (about 5T of onion for 6-8 bagels), toss them with 2 T. of olive oil and put them onto a sheet pan spreading them into a single layer. Place the sheet pan on a lower rack of the oven and roast for about 10 minutes, making sure to keep an eye on them. You want them lightly browned, not burnt.
To add the toppings to the bagels, mix all the dry toppings together. Take the bagels out of the boiling water and place them face up onto a sheet pan. Manually sprinkle the dry ingredients onto the tops of the bagels, very generously. Then by hand, add the garlic and onions, also generously to the tops of the bagels and then proof and bake according to instructions.