I would put the bottom book down straight on the cake board, and decorate. I would then place the dowels on the bottomlayer , place the already iced 2nd book ontop of the first.. then put dowels.. only until the cardboard directly under, and put more dowels for the top layer to rest on. Then drive one long dowel through all layers...
Carboard only on bottoms of each book...
The one in my pix was cake on a board then covered like normal in the fondant for the pages, then I rolled out a large rectangle (cover), set the entire cake on it, and wrapped the cover up and over the top. The four cakes were done this way then stacked (carefully) using dowels like normal. This way looks most like real books because there is no visible board.
Thanks and no problem 
I also should mention that it can be kind of tricky moving that totally fondant wrapped cake and its much easier if you do the whole thing on a parchment on cardboard and transfer it to the fridge and let the fondant on the bottom firm up before stacking.
There was an episode of sugar rush that had Michelle Bommarito as a guest and she showed how to make a stacked book cake. I thought she covered the cake in fondant like normal, not wrapping the whole thing, but the board was still hidden. If you cut the board to the exact size of the cake you can hide it. There would probably be some cake board showing on the underside if you made the stack offset. Before covering Michelle carved out the area where the pages would go, covered the whole cake, and then added a white strip for the pages in the indented area. She scored it with a knife to add texture for pages.
Personally, I am planning to try it this way the next time I have a stacked book cake because I'v already tried it the other way and had some trouble with it. The overlapping fondant for the book cover didn't stay super straight where there was overhang.(maybe there's I trick to this??) Also, when I stacked the cake it was kind of tricky because the dowels sink into the fondant from the above cake and caused some fondant wrinkling. I don't know...it way kind of an off cake for me in general.
Courtney
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