Google Chrome bookmarks are separate from those saved in Google Bookmarks. While it's currently not possible to automatically sync these two sets of bookmarks, you can use a bookmarklet to easily create Google Bookmarks in Google Chrome.

Drag this bookmarklet to the Google Chrome bookmarks bar: Google Bookmark

Any time you visit a webpage that you want to save to your Google Bookmarks page, simply click the bookmarklet in the bookmarks bar.