I love spicy foods. Anything with ghost pepper is going to be gobbled up instantly. I however do not like the negative effects when it comes to getting rid of the waste.
Is there anything you can put in your spicy dishes that maintain the spiciness, but neutralize it during digestion?
There's nothing you can put into the food that will neutralize the spice after you eat it. The only way to avoid the infamous "ring of fire" is to add less spice to begin with. One way you can do this is by removing the seeds. Some of the heat from chilis comes from the seeds, however it doesn't all get extracted from the cooking. After you eat the chili the seeds keep producing capsaicin, meaning your insides get more spice than your mouth. If you de-seed the chilis you need to use more as you lose some of the heat, but you'll get the full force when you eat the food. You can also use chili powder for most of the heat, and then whole or chopped chilis for decoration and texture as the capsaicins from the powder will be more fully extracted by the cooking process.
Some people drink yogurt based drinks (mango lassis and such) to counteract chili. This can calm the heat in your mouth and some people get some relief from the internal symptoms as well, however it's different for everyone and YMMV.
Still, there's only so much you can do, if you like really spicy food you have to be willing to pay the piper.
Capsaicin isn't actually stored in the seeds: It's in the membrane surrounding them. It's a pretty useless distinction, though, since it's pretty much impossible to remove the membrane without removing the seeds as well, and even if you could... why would you want to? Either way, unless you're talking about dried peppers the seeds don't pack that much "punch".
Most of the potency of fresh peppers is found in the white pithy stuff between the seed cap and the outer hull of the pepper. Get rid of all the "white stuff" and you'll have a considerably less spicy dish while still maintaining the flavor of the fruit.
http://en.wikipedia.org/wiki/Capsaicin#Natural_function
If you want something that both tastes spicy AND doesn't upset the digestive system... good luck. In over a decade of professional cooking I've never found something that will reduce the "after-effects" of spicy food, besides some serious antacids.
