You haven't said what airline you intend to use. You didn't write how old the minor is.
You should be able to book this as three separate itineraries. Each itinerary will have its own PNR (passenger name record).
Check ahead of time to make sure there are rows of unassigned seats on the flights you want.
For the legacy airlines (American Airlines, United Airlines, Delta Air Lines, US Airways), you can select seats when you book your flights. You can also change seats by logging in with your PNRs (or with frequent flyer numbers). Thus, even with three separate PNRs, you will be able to get seats together, as long as such seats are available. As an added precaution, you can call the airline after you book your flights, asking to have the PNRs linked to each other. (There's no charge for this.)
If I'm reading your post correctly, the minor is not flying alone, but will meet you in the connecting airport. Rules for minors differ between airlines. In your case, the minor will be on a separate PNR (because of a different itinerary than either of the adult passengers), so the minor will fall under the rules for unaccompanied minors.
Depending on the airline and the minor's age, the fact that passenger is a minor does not necessarily mean that you need to purchase the unaccompanied minor service. For example, on American Airlines, unaccompanied passengers 12 through 17 years of age may travel independently.
Here's what American Airlines has about Reservations For Unaccompanied Minors:
http://www.aa.com/i18n/disclaimers/childrenTravelingAloneChecklist.jsp
Other airlines also have Unaccompanied Minor information on their websites.
I would pick an itinerary with a good, long connection time at the connecting airport to provide plenty of time to meet the minor there. Even then, make a contingency plan for what will happen if your first flight segment is cancelled for substantially delayed.
Domestic airlines in the United States no longer pay commissions to travel agents for flight-only bookings. Unless you have a strong relationship with a particular
travel agency (from previously booking cruises and/or vacation packages), you can't count on a travel agency to work for you for free.
Although the legacy airlines charge a fee for booking tickets over the phone, you can call and ask questions at no charge. If you get a helpful agent, you could get some good advice specific to that airline. (If you get an agent who can't be bothered, call back and ask a different agent.)
