Most of the capsaicin (heat), and bitterness, is in the veins of the chili. The veins are the white supporting structures inside the pepper. Use just the flesh for more flavor and less heat. Considering a whole habanero is ~50x hotter than a whole jalapeno, you would still need to be careful with the amount used. The habanero is my favorite pepper. I haven't used chili in a beer, but have in ginger soda. The bright citrusy taste it adds over other chilis is nice, but easily overpowered by too much heat.
While I haven't researched what extraction method works best for beer, with general cooking my experience has been that more cooking just removes more flavor, but leaves the heat. If extrapolating that to beer works, adding post boil would result in more flavor and less heat from the same amount of chili. Most flavors and especially aromas also seem to be reduced during ferm, so I wouldn't think chili (flavor at least) would be any different.
I assume the alcohol in the finished beer will extract the capsaicin, as well as some flavor. Some mild heating as in a low temp tea, or even steeping in vodka, should also work if you choose a post-ferm/secondary/bottling/kegging addition. It is much easier to adjust the amount of flavor/heat if the addition is done at kegging and starting with small amounts. Think of it like fresh/dry hopping in the keg, only with chilis.
Careful playing around with those things. I don't drink while working with them because drinking leads to peeing, and peeing leads to transfer of capsaicin to places where I can promise you, you do not want it. I now use food handling gloves when playing with peppers.