For those interested in Apple ][ copy protection (and cracking of it) I have found two troves of information.
First is the 4am Apple ][ Library at https://archive.org/details/apple_ii_library_4am Attached to each archive is a text file where 4am describes his cracking process. In most cases he simply follows the boot process, analyzes the often obfuscated code to figure out how to capture the next step in the process, then determines the minimum change required to allow the disk to be easily copied. (e.g. https://archive.org/details/Gumball4amCrack )
Second is PoC||GTFO 0x10 (pocorgtfo10.pdf, available from https://www.alchemistowl.org/pocorgtfo/and other mirrors) which contains an article on various methods of disk were made uncopyable, or at least impossible to copy without being detected.
Finally, http://fabiensanglard.net/prince_of_persia/pop_boot.phphas information on the RWTS18 format used by Prince of Persia. There's also source code at https://github.com/jmechner/Prince-of-Persia-Apple-II
See the comments from http://atariage.com/forums/blog/7/entry-2436-more-apple-musings/and http://atariage.com/forums/blog/7/entry-2514-more-disk-musings/ for previous discussion on this topic.