Basically, ape/ape.S is a traditional BIOS bootloader. It also embeds a GRUB stub, which basically just switches back to the real mode BIOS bootloader entrypoint. So it should work with or without GRUB. The boot sector loads the rest of your executable of disk and prints "actually portable executable" to your display. It then configures standard i/o to use serial uart, sets up the page tables, enters long mode, and calls _start(). That's all I've got working so far. I would love to have e1000 and virtio though!
To try it out, here's how you build the included PC BIOS system emulator and boot an x86-64 ape executable that prints a spinning deathstar:
m=tiny; make -j12 MODE=$m o/$m/tool/build/blinkenlights.com o/$m/tool/viz/deathstar.com &&
o/$m/tool/build/blinkenlights.com -rt o/$m/tool/viz/deathstar.com
See also: https://justine.lol/blinkenlights/manual.html