Whenever I add Shimla mirch to anything I do it at the end..add it, stir, turn off the heat and cover.. let it stand for 10 mins or until serving..
I like it to be a bit crispy. I have an electric stove so even when heat is off the hot plates takes some time to cool down...and this time is just perfect for capsicum to get done..
p.s. even if you don't use an electric stove just do the above and be sure to cover it well..will get done in the steam..
just remembered a tip from a cooking show...when you cut capsicum scrape out the inner wall(inner side of capsicum) a little.. this will prevent it from going soggy..