Only 2-3 system files of AmigaOS 3.9 contains dual PPC/68k code. The rest of the OS is 68k.
What you need to do primarily is to install WarpOS from Aminet and then the PUP emulation system. This way you will have access to both WOS and PUP executables.
Then, you can install PPC native datatypes, mpega.library, etc.