Depending on the chiles, I will scrape the meat out of the skins. I grow one type that is just called "red chile" but they are fairly small so I don't bother scraping them. The larger ones I always scrape.
I agree with you about not using the soaking water, with some chiles. I generally use equal parts fresh water to the chile water.
Did I mention the time Homeland Security searched my luggage because of the two cans of Las Palmas Red Chili Sauce I had inside?