I always like to add some or all of the tomato before adding the meat back into the pot. Let the tomato caramelize a bit. THEN deglaze with beer/stock, add the meat back to the pan, and simmer away.
Personally, when I use cocoa powder, I add it with the dry spices. If I use bar chocolate, I add it towards the end to let it melt into the liquid.
Peace, Love, and Vegetable Rights!
Eat Meat and Save the Plants!