Add onions, chipotle in adobo, water, and lime juice to bottom of slow cooker. Add chuck roast. Sprinkle seasoning over top. Secure lid and cook on low for 8 hours.
In a sauce pan over medium heat, add pinto and black beans, along with taco seasoning. Stir occasionally and slightly smash bean while allowing to cook for about 20 minutes.
In another sauce pan over medium high heat, add water, salt and rice. Cover with lid and cook about 20 minutes.
At the end of the cook time, remove any bones (if there are any) and then shred meat.
Start with tortilla on flat surface. Add two slices to center of tortilla. Next add portion of bean mix, sprinkle with cheese, then portion of rice. Then add shredded beef and again sprinkle with cheese. Fold in sides of tortilla and roll up top to bottom. Repeat with remaining tortillas.
In a large saute pan over medium heat, toast each side of the burritos, starting with the closing flap, for about 90 second. Repeat with each burrito.
In the same pan, add portion of cheese in a single line about the length of the burrito. Once it has melted down some (about 30 seconds), place burrito on top of cheese. Let melt another 30-60 seconds, then remove. Depending on size of pan, you should be able to do two at a time. Repeat with remaining burritos.
If desired, wrap each burrito in aluminum foil for presentation.