I've done something like this before (in a Belgian quad), but I actually added the cherries after the boil and left them in for 15 minutes...basically trying to sanitize the fruit. Then I cooled off the wort with an immersion chiller, and put everything into a plastic bucket for the primary (no way I was going through the hassle of getting cherries in and out of the carboy!). About seven days in, I scooped the cherries out with a sanitized strainer, and then the fermentation continue.
I wouldn't swear that this was the right way, but I was pleased with the outcome.