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That depends very much on what bootloader you are using. The GRUB boot menu is stored at /boot/grub/menu.lst. The LILO boot menu is usually at /etc/lilo.conf, but it can vary by distributions.

Specifying the new kernel should be pretty obvious for both of them. A GRUB entry should look like:

title What you want the option to look like on the menu
root (hd0,0)
kernel /boot/vmlinuz-2.6.50-27.8
initrd /boot/initrd-2.6.20-27.8

You should copy any kernel options from your old one onto your new one as well.

LILO should look something like:
image = /boot/vmlinuz-2.6.50-27.8
root = /dev/hda1
label = Whatever you want the option to look like on the menu
append="kernel options"
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Q: How do you edit your bootloader to point to the new kernel?
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