Organizing an entire house is too much to think about at one time. One a piece of paper, map out the activities and "stuff" you need for those activities. Spend a day getting all the "stuff" in the right room. Forget about what it looks like for now. Choose the function of the room first before concerning yourself about it looking nice.
After you have everything in its general location, take an inventory. See what you have multiples of, what is broken beyond repair, and what you still need storage containers for. I'll guide you through the rest of the system next week.