If you really used the 6000dpi scan setting you can simply use your photos as they are. The photo books need only 200dpi for a decent print.
If you have a 3x3 inches photo scanned at 600 dots per inch, your photo has 1800x1800 pixels. Apple's photo books will print it at 6x6 in the book without a loss in quality. You could put it also into a 9x9 photo box, since the 9x9 version will still have 200 dpi.
The photo books in Photos will scale the photo so it fits into the photo boxes, and all is fine, as long as you are not seeing an triangles with an exclamation mark on some of the pages.
If you are not certain, if your photos have enough pixels, open the info panel for a photo. select it in Photos and click the ℹ button in the toolbar or use the key combination⌘I . The Info panel is showing the pixel size - width and height. divide the width and height in pixels by 200 and you will know the maximum width in inches that you photo can be printed in a book. My photo below could be printed at roughly 13.5 inches times 18.2 inches.
