My rules are:
Everything I cannot live without goes in the handlebar bag: passport, wallet, iphone etc. It also contains stuff I need off the bike or need quickly, so wash kit, rain jacket and first aid, snacks
Saddlebag left pocket contains tools and tubes, right pocket has food, noodles, couscous, honey, tea
Main compartment has layers consisting of clothes and sleeping mat, and cooking kit with gaps stuffed with socks, underwear etc.
last things in are compression sacks with sleeping bag and tent fly and my kung fu shoes.