TWOV questions

Hello!
I would like to fly to Beijing (depart early Sept 18 from Brisbane)
Arrive late in Beijing and stay 3 nights leave within 72 hour TWOV
Fly Beijing to Hong Kong and stay 2 nights, no entry permit required
Fly Hong Kong to Shanghai and stay 2 nights leave within 144 hour TWOV
Board a cruise from Shanghai on Sept 26 which travels to ports in Japan > Korea > returns back to Shanghai (6 nights) on Oct 2, I will fly back to Brisbane on this day.

My question is: how do I book my flight paths to qualify for all of the transit without visa exemptions?
Is it possible to have multiple flights booked, such as Beijing > Hong Kong and Hong Kong > Shanghai as domestic flights, and a separate round trip ticket back to Brisbane, even though I start my trip in Brisbane to Beijing and leave Shanghai to Brisbane.

Sorry for any confusion.