You can in fact link all of your bookings together. The ones booked through the outside agency will simply have to be requested by that agency to be linked to the ones booked through the cruiseline direct. Hopefully those with the online bookings didn't use an agency where you just click on a cruise and put in your credit card. Many online agencies have 1(800)#'s and agents on the other end of the phone line so you can call and request them linked. I'ts called "Cross referencing your dining".
If some in your party booked with an online agency that has no phone # and no agent contact tell them to never do that type of booking again. Without a person and extension of who that person is, what will you do in the event of an emergency and you need to cancel? What if you need to be notified of an itinerary change, who whould do that? You need to deal with a live human being for a booking. Either at the cruiseline or through a local travel agent or one of the many online agencies that provide personalized service.
If it was in fact an online click and book type booking you're out of luck. No way to get them to cross reference your bookings and the cruiseline can't even touch their bookings.
One last thing you may be able to do... Try calling the cruiseline back if it is an online only booking and ask if you can have the booking transferred to another agency or RCCL. They may require you to send a written request, you can do this by fax. If it's in penalty even this may not be possible but it's worth a try. Once transferred they can cross reference all the bookings. Online is a fine way to book and sometimes you can save $$$ but be sure if you do that you still get an agent that is knowledgable, friendly and responsive to your needs.