Rinse the chipotle chiles and drain. Place in a medium saucepan and cover with water. Set over medium-high heat. Once the water begins to simmer, cook for 15 minutes. Turn off the heat.
Place the stemmed and seeded ancho chiles and tomatoes in a pot and cover with water. Simmer for about 6 to 8 minutes until the tomatoes are cooked through and soft. Transfer to a blender with 1 cup of the cooking liquid, and puree until smooth.
In a large saute pan, heat the oil over medium-high heat until hot but not smoking, about 1 to 2 minutes. Stir in the carrots and onion, let them season for a couple minutes. Make some room and add the garlic, cook for another minute. Pour in the ancho chile and tomatoe puree, the marjoram, thyme, bay leaves, salt and sugar. Stir, and let the sauce season and thicken for 5 to 6 minutes.
Pour in the vinegars, and cook for another 5 minutes. Finally, drain the chipotles, discard their cooking liquid and add to the mix. Let it all cook together for 5 more minutes and turn off the heat. Let them cool off and place in jars.
Cover tightly and refrigerate. Give them a day before you eat them, so they will have had time to pickle and thrive in that adobo sauce.
They will keep in the refrigerator for 6 months, if you don't eat them all first.