Use systemctl to set default runlevels. Assuming you have bash-completion package installed, you can type systemctl set-default, then double tab to see all targets available:
$ systemctl set-default
basic.target local-fs-pre.target runlevel2.target
bluetooth.target local-fs.target runlevel3.target
busnames.target mail-transport-agent.target runlevel4.target
cryptsetup-pre.target multi-user.target runlevel5.target
cryptsetup.target network-online.target runlevel6.target
ctrl-alt-del.target network-pre.target shutdown.target
default.target network.target sigpwr.target
emergency.target nfs-client.target sleep.target
exit.target nss-lookup.target slices.target
final.target nss-user-lookup.target smartcard.target
getty.target paths.target sockets.target
graphical.target poweroff.target sound.target
halt.target printer.target suspend.target
hibernate.target reboot.target swap.target
hybrid-sleep.target remote-fs-pre.target sysinit.target
initrd-fs.target remote-fs.target system-update.target
initrd-root-fs.target rescue.target timers.target
initrd-switch-root.target rpcbind.target time-sync.target
initrd.target runlevel0.target umount.target
kexec.target runlevel1.target
You can see there are runlevelX.target options available, these will work similarly to the init runlevels.
As for the file location of startup configuration, Ubuntu 16.04 LTS uses systemd. Under /etc/systemd/system/ directory you will see a symbolic link named default.target which points to the current default target. I strongly advise using systemctl set-default over messing with the files/directories/links.