You cannot get a single itin to show up online if the connection is over 6 hours. Let me tell you about how the connection I took in FLL over Christmas was 6 hours and 4 minutes ... you can call and book it as segments though. However you won't get extra points for booking online and you will pay the phone booking fee.
Also if you are booking mixed class tickets you are often better to book separately anyways as the pricing for the non-mint leg is insane if you book as all one trip. As for protecting your flights, I am not sure what the official policy is.