I like to chop these up pretty small. The idea here is that once they're cooked down they'll just dissolve into the matrix of the chili, all very zen- like. The real problem here is the onions. I have an old pair of motorcycle goggles that I use for woodworking that I wear when chopping onions and that seems to help. My aunt used to swear by holding a burned match between her teeth.
Folk remedies abound here.
Try what works for you. The best I can suggest to space them out. Wash the green peppers, cut out the stems and dice them. Put all this stuff in one big bowl. This should be left pretty chunky.