Booking Multiple Itineraries Online

Perhaps some of you more frequent flyers might be able to suggest an online web site that allows one to book multiple itineraries for family travel. I will once again be bringing the entire family to Thailand over the summer, but there are three different itineraries for the four of us that must be co-ordinated as the wife and kids will be leaving before me with one of the kids returning with me while the other kid stays a month longer with mom. I fear that if I book online a ticket where one leg must co-incide with another intinerary then I risk not being able to book the second ticket on that same flight. I have only found websites that allow the booking of one itinerary at once. I ask as for the first time the online sites are offering substantially less expensive fares than my traditional Chinatown travel agency.

Thanks in Advance