In the electric stand mixer fitted with the paddle attachment add the water, butter, honey and soy sauce. Run the mixer on low for 1 minute. It won't be well blended, just stirred around the bowl a bit.
In a large bowl, whisk together the white whole-wheat flour, all-purpose flour, dark rye flour, manchego, 1/4 cup pecans, quinoa, sea salt, cracked pepper and paprika. Add to the mixer and run the machine on low until the mixture just comes together and is blended. This shouldn't take more than 1-2 minutes.
Lightly flour a surface and set the dough on top. With lightly floured hands shape into a disc, cover with a tea towel and let rest for 15 minutes.
Preheat the over to 350F and place a rack in the top third of the oven, at least 6-inches from the heat source. In a small bowl combine the 2 tablespoons pecans, chives, sesame seeds and poppyseeds. Line a baking sheet with parchment paper and set another piece of lightly-floured parchment on the counter to roll the dough on.
With a lightly floured rolling pin, roll the dough to 1/8- to 1/16-inch thickness on the lightly floured parchment paper. If you have a silpat, place it beneath the parchment to keep it from sliding around the counter. The thinner you roll the dough, the crisper the crackers will be. If the dough starts to bounce back when rolled, let it rest for 5 minutes and try again. Wait until it doesn't resist being rolled out, to roll it out completely. When it's just about at the desired thickness, sprinkle the chive mixture evenly over the top. Roll the rolling pin one more time over the top to set the mixture into the surface of the dough. Sprinkle with sea salt flakes. Transfer the dough on the parchment to a baking sheet and chill for 10 minutes in the freezer or 15 minutes in the fridge. *I use large 16X22 baking sheets. If you have smaller ones, separate the dough into two mounds and roll out on two separate pieces of parchment so that it fits onto your baking sheets for chilling.
I like to use a 1-inch-ish circle + slightly larger, fluted, rectangle cutter and cut as many crackers as possible. Re-roll to get as many crackers as possible. If you notice thick spots in the dough as you're cutting the crackers, roll it thinner.
Bake for 20 minutes in the top third of the oven. Check around the 15 minute mark for doneness...they will be done sooner or take longer depending on the thickness of the dough. You want them bronzed up a bit and crispy. Let cool on the baking sheet. Once cool, store in an air-tight container until using.