Grub2 configuration is in /etc/defaut/grub ( on Debian at least ).
Set GRUB_DEFAULT=saved in /etc/default/grub if you want to start with the last good boot.
update-grub - detects kernels automatically and writes boot lines to /boot/grub/grub.conf
grub-set-default - set the default entry
grub-reboot - set the boot entry for the next reboot only ( for testing new kernels or other boot stuff especially when you're working remotely )
First boot entry is number 0