I've booked our 2-year-old separately at least three times now. The "best" way to do it is to call and book over the phone. If you explain that you can't book it online because the child is a minor and can't be booked without an adult, they will waive the phone ticketing fee. (If they don't, try a different agent.) Booking over the phone will hopefully ensure that the child is booked as a child, won't be separated from you, etc. (Then again, I believe the phone agent booked our kid as an adult the last time we did this... though we had no problems.)