I do a vanilla porter with mulatto chilies. The local spice shop owner (Savory Spice here in Boulder) works with brewery's like Avery's, Left Hand, and Oskar Blues. The guy knows his stuff! He suggested to me just to cut them open on one side to get more flavor and then throw them in right after the boil to disinfect. It's worked great for me!
To give a guide, the mulatto chilies are what he called "a 1 or 2 out of 10" on the hot scale and I find that 2-3 give just enough to where it's not too spicy that it overwhelms.
Hope it helps!