I have a similar setup. I recommend that you boil the extract and chiller, for at least a few minutes to fully sanitize them. For Example, I like to stop the boil and the clock, with about 15 mins left, and add the extract with the flameout. Then I turn the gas back on, and start the clock, when it starts boiling add the chiller. Everyone has a different method, but I like this method because it ensures that I sanitized my wort properly.