This is a GREAT question. It gets right to the heart of my biggest concern for this entire school year! When Kylee was younger, I would simply wear her on my back during school time or we would work on school things during nap time. We had our school supplies in a different room with a door that we just closed so she couldn't get into things.
Now our materials are not only accessible during school time, they are accessible ALL the time because they are in our living room. Technically we have an office that we could cram them in to, but for a variety of reasons that isn't the best idea right now. We did set aside one shelf in the office for things with many small pieces that would be inconvenient should she decide to use them for dumping practice.
All of this, however, doesn't get to what she actually does do.
Mostly she joins in with us. We start every school day with a short group time (song, story or lesson, prayer) and this is really for the younger kids. It gives them practice sitting quietly which is practice for Sunday School and other places. I have found that after a period of focusing intently my younger ones are more able to go off and be independant for a short amount of time without demanding my attention while I go through the daily plan for the boys and give assignments (well, to Aidan).
When the boys are sitting at the table with work, she will often sit in her booster chair and ask for art supplies. This week she has done crayons, markers, and stamps. I hang her art near the infant/toddler work shelves.
That would be the third thing she does...work with materials. I give her occassional presentations on infant/toddler materials that are aimed at her level, but she will also take out the knobless cylinders for stacking, the small objects to name, and other things. I don't let her take out the puzzles or other more breakable things, but as long as she is being respectful I do let her use the beginning sensorial type things. One neat thing that has happened this year is that after watching the boys use a work rug, she is now using one spontaneously. She takes it out, spreads it out, brings the material over, works on it, then puts things away. We are still working on rug rolling skills, but she is generally adamant that she wants to do it herself (she is two).
Of course she has her moments. She isn't so great about not disrupting our longer reading when there aren't pictures, but I encourage her to wander off and play with her babies or do something else when that happens. There have been a few dumped materials, but nothing we couldn't pick back up. She doesn't always remember to put her work away on her own, but she is cooperative about going back and I can see how this habit will serve us all well!
Mostly Kylee sticks with us. If we are in a group lesson she will observe, if we are at the table she will do art, if the boys are working at the floor she will as well!