where the hardware can do either, the kernel you boot chooses the cputype to suit itself.

/sys/src/9/pc is only 386 (ie, 32-bit x86). another directory is used for amd64 (ie, 64-bit x86).

you can use the 386 kernel to compile and install the /amd64 environment though,

which you'll need to do before running an amd64 kernel.