First of all I would sort through their things and discard anything that is broken. Then,if there aren't any more children in your future,donate things that your son no longer uses and that you wouldn't pass down to your daughter. Doing those 2 things could eliminate alot so you have a good starting point.

Your sons small things can be grouped by category(all action figures in their own clear plastic shoeboxes). The same for cars. My son has alot of HotWheel size cars and they actually make cases with slots for each car and hold about 30 or so cars per case and stack on top of each other. We got ours in the toy dept. of WalMart.
Since your daughter can't read,taping pictures or actual photos of toys on the outside of clear plastic shoeboxes will help her know where her things go. Example: tape a photo or drawing of blocks to the outside end and she knows to put only blocks in that box) That will help with any of her small toys. The larger toys can be rotated. If you have a basement or garage or attic,etc store them there and only have a couple out for 2-3 weeks then rotate them. Most kids only play with 20% of their toys about 80% of the time anyway. If you live where it is warm,can some of the big toys go outdoors on a deck or driveway or shed? She doesn't need all her dollhouses out at once,rotate those as well. It keeps the selection like new when she gets a different dollhouse after 2-3 weeks of having it out of sight.

Hope these tips help. If you think of anything more specific let me know.