Inside the "...\Chrome\User Data\Default\" directory are two files. "Bookmarks", and "Bookmarks.bak". One is for your current bookmarks, and the other one (with the .bak extension) signifies that it is a bookmarks backup, if anything goes wrong. Bookmarks.bak gets overwritten every time you close Chrome.
Bookmarks in Chrome exist as a virtual filesystem. Meaning, that all your bookmarks are really just stored in one file, but appear as an actual filesystem inside Chrome.
You only have to copy that file, and back it up somewhere. And if you want to recovery your bookmarks, simply copy/paste the "Bookmarks" file you backed-up, back in to the directory you took it from.
Chrome must be closed prior to doing this.
Hope this helps.
(and btw, try opening the "Bookmarks" file with a text editor like Notepad =])