This part is easy. From the previous step, you should have ensured that you have some slop aroud the image of the page you are interested. This allows you to crop later, which is especially important if it is a thick book or magazine.
The way we prefer to do this is to shoot all the right-side pages first, and all the left-side pages second. Shooting all the pages this way simplifies post-processing later.
Below, you can see Matti shooting all the right-side pages of a book. He places the glass, presses the shutter button, replaces the glass, presses the shutter button... ad nauseam. Do this until you have reached the end of whatever you are interested in scanning.
Then flip the book.
Continue as before, but now shooting all the left-side pages.