A.P.
I agree with the last poster. My sister has 5 kids and that is how she's always done it--plastic bins with "Choking Hazards" written on it--they are sorted by type (legos, etc.) then put up on a high shelf. Her kids learned over time that they need to ask for those bins when they want them, and then put the things away as soon as they are done playing with them. I like the last poster's suggestion to have her play with the toys when the baby is sleeping.
I'm in the same position as you are, and I haven't been doing a great job of doing this myself. I'm also not sure my son would really "get it" and be good at keeping the pieces together and picked up. But I always try to scan the room I'm in for choking hazards when I walk in, so that I can pick them up and put them out of the way.
Good luck.