In preferences -> Drawing Attributes, there's a checkbox for 'Uniform Pens & Colors'. With this box UNchecked, drawings will have the pen settings they have in AC. If the box is checked, all the drawings and layouts use the Pen settings defined at Options -> All Pens & Colors. They will be independent from the AC settings.
You can apply your AC Pens to the layout book with
this great tip of Link's. If you want your pens to always be the same as AC, go ahead and do this tip; then it doesn't matter if the box is checked or not.