You can also compile many applications yourself as the source code is often freely available. This is likely to be necessary if you want to use an application that is not maintained by either the RedHat/PPC or Debian teams, as the application author(s) would probably only supply a precompiled version of the application for the ix86 architecture.
Some applications need Linux header files to build. These are normally found in /usr/include in the directories asm and linux. When using Linux/APUS the header files installed by e.g. RedHat/PPC should be OK for most applications. However, if you decide to replace the default header files with Linux/APUS specific header files you must also include the directory /usr/include/asm-m68k which must be either a copy of the linux/include/asm-m68k directory or a link to it.