Anchors are a very useful aspect of interactive ebooks. Essentially, they are local links within your ebook that you can use to perform various tasks. Mainly they are used to give a reference point for a link. You can also use them as reference point for chapters. Instead of splitting chapters into their separate files you can have a large HTML file containing your entire book and reference the various chapters and subchapters basically by automatically scrolling to them.

Adding an anchor

Click on the Anchor tool. You will be met with the Insert/Edit Anchor window.

Simply add a unique name for reference to this particular anchor and click OK. This will create an anchor wherever in the ebook your cursor is. A flag will be added in place of the cursor as shown below. They can be removed like text or clicked on to reopen the Insert/Edit Anchor window to edit its name.

You can then link to this anchor by adding links or through the chapter by editing a chapter's properties. 

Another way of utilizing the Anchor tool is by first highlighting text and then adding an anchor. This will enable a slightly different insert/Edit Anchor window.

With the options of:

Create a new linked chapter this anchor
A new chapter will be created titled after the selected text, and will link directly to this anchor.
Make it a child of the current chapter
The new chapter that will be created will be a subchapter of the chapter the anchor exists in. And will automatically increment the anchor name in case of adding another subchapter anchor within the same chapter.