Cook beets by cleaning, wrapping in foil and baking in a 400º oven for 45 min to 1 1/2 hours, depending on the size of the beets. They are done cooking when they begin to feel soft when you squish them (they're hot - use an oven mitt). Allow to cool for about an hour before you begin the pickling process. If you're in a hurry you can also find precooked beets in the refrigerator section of many grocery stores.
Make a spice pouch to flavor your pickling juice by doubling over a piece of cheesecloth, placing your cinnamon stick, whole cloves, allspice berries, and mustard seeds in the middle. Bring the corners of the cheesecloth together and tie with butcher's twine.
To make the pickling juice, in a large saucepan combine white vinegar, water, organic cane sugar, salt, and spice pouch. Stir until the sugar is dissolved. Simmer for 5 minutes.
While the pickling juice is simmering, peel and rinse the cooked beets and cut into 1/8 inch slices. Also thinly slice your white onions.
After the pickling juice has simmered for 5 minutes add the sliced beets and onions to the saucepan and bring back up to a simmer, then remove from the heat.
Allow the beets to cool, remove the spice pouch, and pour the pickled beets into a glass jar. Store covered at the back of your fridge for up to one month, but I doubt they'll last that long!