If you're using the minimum installation CD you'll be fine. And you'll be installing Gentoo the Gentoo way
(meaning you do everything from the commandline, no automatic installer). Basically, follow the installation instructions on the website, and when it comes to installing your bootloader, you can just skip it. Copy the kernel/initrd etc to your existing /boot partition and then edit grub.conf to add gentoo. You should be good to go. You'll only kill your bootloader if you specifically choose to install a new grub yourself. There's nothing automatic about it.
The only thing you should be careful of is partitioning. That's about the only danger you'll face.