You could read the entire OS ("KERNAL") and BASIC disassembly start to finish (there were books listing them, with comments added). You could systematically test what changing registers would do - I remember pestering my parents at work by calling them to let them hear what sounds I managed to make by randomly POKE'ing things into the sound registers just to experiment.
And of course the manuals. While I agree with you books were hard to get, the C64 manual was fantastic.