We have an eat-in kitchen with a large table that we're using to homeschool. I cleaned out the cupboard closest to it and deemed it for school use only. It has our books, notebooks, and any other must haves for homeschooling. I use mason jars to keep our art supplies organized. They are a nice size and it makes them neat and accessable to the children, I just push them back far enough on the counter that the little ones can't reach.
I bought a cart that has a dozen little drawers and organized it for craft supplies and paper, and also for activities for the little ones- one drawer has playdough and appropriate toys, one has color books, one whole drawer is just crayons, one drawer has our science equipment (magnifying glasses, etc), one drawer has math manipulatives, one has writing paper, etc, etc.
The drawers pull out so it's easy for me to grab the playdough or crayon drawer and bring it to the table, then the kids can put everything back in it at clean up time and I go put it back into the cart. On the top of the cart we keep all our nature study things in nice baskets.
I also keep a basket of the books we all read from- the bible, the catechism, the book of virtues, the lives of the saints, etc, by the couch. It makes it accessable in the morning and I can nurse the baby while I read and not have to keep jumping up to get something out of the cupboard.
The remainder of our family library is downstairs in the office, on a bookshelf, grouped by subject. That is also where I keep anything else that won't fit in my cupboard upstairs- additional resources and art supplies, paper, large maps, etc. Our printer/copier is down there, too.
It took me somet ime to get this organized, but it has been worth every minute of work. There is nothing that compares to being able to run downstairs and grab what I need in seconds. I spend 15-30 minutes every night after the children are in bed prepping for the next day.
I don't know how Seton works, but I have given my six year old a binder that is his. He has a section with writing paper for copywork, a section with graph paper for working his math problems, a section with science experiment print-offs, a section for his first holy communion prep papers, and a section in the back with his time line for his Book of Centuries. I thought this would work better than dividing his binder by subjects, and so far it has.
I have my own 'control' notebook where I keep a master of our weekly schedule, including blocks of time devoted to each subject and reoccuring appointments (like playgroup and story time), my lesson plans, sleeves to hold handouts for each child, a list of things I want to accomplish this year for each child, a section for things I need to do, and a section for things that inspire me.
Our day is broken into 'blocks'- one for each subject. Each block is only half an hour long. We do religion and language arts on the couch first thing in the morning, then an hour outdoors for nature study, fine arts (Latin, music, or art depending on the day), math, and then history before lunch. After lunch the children have a mandatory rest period (and so does mommy, who needs it desperately by then!) then a mandatory outside play time. After playtime we have a short read aloud time, either a book about the lives of the saints or something similar (right now we're reading The King of the Golden City for my son's FHC prep)
From 2-4 they have free time to finish their school work or do other projects, art work, or independent reading. If they have nothing else to do, they may spend their afternoon outdoors or playing with their toys. I am available to them during this time, but they are obligated to work on their own as much as possible. I make a point of doing whatever teaching is required of me during our half hour blocks in the morning. We always move on to whatever is next at the end of the half hour and they can complete any additional work they have in that subject during the afternoon. This frees me up for housework, time to spend with the little ones, or time to prepare for tomorrow's lessons.
This blog has helped me a lot, particularly her posts on the learning spaces (look down along the right side)