General rules of thumb:
1) Keep things that may get wet (shelter) apart from things you need to keep dry (sleeping bag, insulation).
2) Think about what you may need to access during the ride, e.g jacket. Once packed, I tend to leave my seat pack as something that doesn't get opened during the day (depends on style of bag).
3) Weight low down, bulky but less dense up high (so tools and tubes in frame bag looks like a good idea).