I have each of my projects in a small clear plastic tote with the pattern on top, and the thread I bought for the fabric in the tote.
When I finish a project, I put all the scraps into my "scrap" bag, which is really just a recycle grocery bag. I want to buy a tote for my scraps, just money too tight right now.
I have childrens' fabrics all together in one section of my sewing room.
I only buy when I am getting ready to start a project (though I buy more than one project at a time) and don't buy in-between. This keeps my stash smaller.
My project totes are stored on head-high shelves in my sewing room. They are just the size of shoe boxes and the next size up.
I have mechanics bins on the wall that have see-through covers on each section, I use these to store my used thread when I finish a quilt. I check it before I buy more.
My stencils are on a pegboard on the wall, along with my rulers. I keep my rotary cutter on top of my cutting board on my little card table in the room.
I have a big quilting frame in the middle of the room.