My craft room is 1/2 toddler and baby play area (I have a 2.5 yr old boy and a 6 mo old girl) and 1/2 craft space. What I do is have bookcases - some with doors and some without - lining the walls on the craft side. On the other half of the room, my son has a train table. It has his train stuff or other toys on it almost all of the time but it looks contained being on the table. And then the other toys, we have those plastic milk crates that sit under the table to keep them out of the way. Then we have things like a bouncer, etc near the train table. My son normally plays at his table or on the floor near by but things stay pretty contained that way. I can also give him crayons and coloring books, etc and he can color at the table while I'm at my craft table (though often he wants to sit at my table too).
So, I'm not sure if that is helpful but I find having a dedicated play table and storage underneath works well for us.