It really comes down to your personal travel style and preferences, as well as how willing you are to do the research yourself. Some people love to do the advance planning on their own - some don't.
You'll obviously save a lot of money by doing as you suggest - basing yourself in Cairns and Airlie Beach and booking day tours from there, but it would require that you book your own accommodations and be willing to be mostly independent - picking and choosing what you want to see and do rather than relying on an all-encompassing tour provider to do that for you ... and then having to live with their choices and agenda.
There are numerous day trip and tour providers in both Cairns and Airlie Beach that would likely answer your needs and generally satisfy your curiosity about both places. Might suggest looking at the Trip Advisor pull-down menu under "Things to do" in both locations and see if any of the offering appeal to you and then decide.
For flight planning I generally start with Google Flights to sort out the various options, then book directly with the airline. For info, both Virgin Australia and JetStar offer low-cost options for getting around the country.
For accommodations I usually start with Booking.com. Their filters are quite helpful in narrowing down the various options based on my preferences regarding location, price, amenities, etc. Do read the fine print regarding cancellation policies - some places are pretty liberal in that regard, others not so much. It's worth checking the website for a specific hotel or B&B that appeals to you - can sometimes find better prices, more amenities, etc. by booking direct.
None of this is as daunting as it sounds - just takes a bit of dogged determination and the willingness to do the legwork yourself.
