The beans just follow the instructions on the package for soaking and cooking them. The only difference between them and the store bought ones after soaking and cooking will be what you cook them in. If you buy "chili beans' from the store they are cooking in chili spices before canning. So, once you cook them in your chili, they will be your own 'chili beans'. As for the tomatoes, I just cut em up and make sure the juice and all go into the pot.
You are going to need a good tomato paste base, so this is where a good food processor comes in handy for making your own tomato paste. Well, OK, mine does anyway. Others may come along that have different recipes where you might not need a paste base. Other than that, just use fresh peppers and good meat (I like a cut up chuck roast for mine).