Yeah, I wouldn't put boiling liquid in the fermenter. Just boil the 2 gallons of water, add the LME and let it cool. Then pour in the fermenter with the rest of the water.
I've never used fruit or extracts, but I would not put it in the primary. I would put it in the secondary after it's done fermenting, starting only with a little. If it's not enough, add a little more at bottling time.