You should have a lot of onions. If you add them all at once it will be a giant pain in the stirring butt, so add a few handfuls at a time. Stir for 1-2 minutes, until they start cooking down a bit and turning translucent. Repeat until you've added all the onions. Season with salt and pepper.
Reduce the heat to medium-low and continue stirring occasionally to prevent sticking. After 15-20 minutes they should be a beautiful blonde color. For future reference, if you want to make French Onion soup this is how done the onions should be.
Check your pan, if you have some dry spots it is time to throw in a dash of water. The onions will reabsorb this. Continue cooking and stirring for another 15-20 minutes. They will be a beautiful golden color. You could use them at this point but I prefer them to be slightly crisp and dark around the edges. To achieve this you need to stay put and stir them for another 10-15 minutes to make sure they crisp and don't burn. Just before doneness add the ½ tsp. fresh thyme leaves and 1 Tbsp. balsamic vinegar. Cook for at least one minute. Use it to deglaze the pan, if need be.
In between caramelizing your onions preheat the oven to 425℉. In an oven safe dish, that will hold 3 cups, mix the 8 oz. cream cheese, 1 c. sour cream, zest of one lemon, and a dash hot sauce until fully incorporated. Fold in the 6 oz. Gruyère Cheese, most of the 2 scallions, and onions.
Place the dish on a lined cookie sheet and bake for 15-18 minutes. About half way through check to make sure the Gruyère is melted in, if desired, give it a quick mix and continue baking. When it is done you will see bubbles and browning.
Top with extra scallions and serve warm.
Notes
Nutrition calculated for the recipe at happyforks.com/analyzer/