i use the packing cubes too and have found them very useful. the ones i use have two compartments, so i stuff the dirty clothes to the other side as I go along. it works well for small things at least. i have three in different sizes, so shirts in one, pants/longer things in the largest, and underwear/bathing suits in the smallest. its also really easy to find things.
i usually slide any books/guides in along the sides or at the bottom. i also roll a lot of things into tight little tubes and then stack them side by side on top of everything...my towel, jacket, sarongs, things i might grab a lot and not want to unload for. my pack zips open all the way around so i can shove things down as i zip it shut. my toiletry kit goes near the top at the small of my back. in the end everything has its place. i also use my fleece jacket as a pillow and stuff it with my dirty clothes (that aren't too stinky!) from the night before.
i always take a couple ziplocks and plastic shopping bags too, you never know when you'll want to keep something dry! good luck and happy travels!