To answer your questions:

1) You can either bookmark an entire topic (bookmark the page URL while reading a topic) or if you want to go to a specific reply in a topic chain, you can click on the message icon (usually the white paper icon in the top left corner of the reply, but it can be other symbols), and then bookmark that page URL.

A topic bookmark will look like this:
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A reply bookmark will look like this:
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2) Just clicking on a topic marks it as read. There is a "Mark All as Read" button in the Topic list, so you can read the ones you are interested in, and then click the "Mark All Read" button to clear the rest of them, so that next time you log in, only new topics since that point will be highlighted.