It is far easier to get the HQ down in 1 pass using the 2000 lb bombs. Obviously, more than 1 flight of bombers is needed if we're speaking of B24's or Lancasters. I have not tried using the 4000 lb bombs from the B29's yet, but I can assume the same logic applies.
Unless the bombers are using historically accurate bombing speeds (220-240 TAS), then it would be very difficult to drop all 14 1000 lb bombs on top of the HQ, even then I think it would be easier to use multiple set of bombers.