To boot Nautilus on the Phi, first compile Nautilus for it by running

$> make menuconfig

then in the platform selection, select the Xeon Phi

Then use the phi_console utility to boot it. Run phi_console with no 
options to get a help screen. Here's an example of using it to boot
with the weever bootloader

./phi_console -m 1 -b /sbin/weever -k nautilus.bin

This boots the phi using Phi card 1 with the Weever bootloader and Nautilus as the kernel

Instructions on how to navigate using the console appear on the screen