Since China reopened to foreign tourism in the early 1980s, all foreign tour operators have been required to use official state-registered travel companies as ground handlers. All arrangements in China were usually put together by one of three companies: China International Travel Service (CITS), China Travel Service (CTS), or China Youth Travel Service (CYTS). Controls are now loosening, foreign tour companies are now allowed some limited activities in China, and the range of possible Chinese partners has increased, but in effect, CITS and the like are the only companies with nationwide networks of offices, and most foreign tour companies still turn to them. They work out the schedule at the highest possible prices and send the costs to the foreign package company, which then adds its own administration charges and profit margins and hands the resulting quote to you. You could get the same price yourself by dealing with CITS (which has many offices overseas) directly. But you can get far better prices by organizing things yourself as you go along so, other than convenience, there's little benefit and a great deal of unnecessary cost to buying a package. Just about any tour operator will offer to tailor an itinerary to your needs, which means it will usually simply pass on the request to one of the state monoliths, and pass the result back to you. The benefit of dealing with the Chinese travel company directly is that you cut out the middleman, but if things go wrong, you will be unlikely to obtain any compensation whatsoever. If you book through a home tour operator, you can expect to obtain refunds and compensation if this becomes appropriate. In general, however, when organized through CITS, rail or air tickets for your next leg are reliably delivered to each hotel as you go. Never book directly over the Web with a China-based travel service or "private" tour guide. Many are not licensed to do business with foreigners, have not been licensed as guides, or will hugely overcharge and frequently mislead you (in the most charming way possible), and you will have no recourse at all.
If money is no object, then start with the list of tour companies below, nearly all of whom will arrange individual itineraries; or contact the CNTO to find properly registered Chinese agencies who may help you. The Hong Kong Tourism Board and the Macau Government Tourism Office, in whose territories the tourism industry is well regulated, can point you towards reputable operators and talented licensed private guides.