Okay, I feel your pain. I used smaller totes and cut the pictures off the boxes and taped them to the outside for clear identification. If the train set is really huge, use one tote for track and the other for cars and other accessories, or stick with your existing large totes for this. If you don't have the original box, then take a photo of the pieces or cut out something from one of the circulars or from the on-line site, and stick it on the outside of the tote. Kids who can't read can look at pictures. I use clear package sealing tape so it's too thick for the kids to peel off.
The next trick is, the kids get to play with ONE of these toys at a time, and they can't break out another one until this one is picked up entirely. Put some of the totes in a closet or the basement if you have to, to limit the choices. A new tote comes out when a previous one gets put away.
Let the kids figure out how to put things together even if you can't. That's the point of these toys. If they don't enjoy it or can't figure it out, it goes back in the tote for a month or two. If the in-laws want to know how it's going, they can come over and bond with the children while working on it!
We set up a spot in the basement with a special table for the track sets. All the totes went underneath the table. You could even buy a folding table at Walmart or BJ's that has adjustable legs and then the youngest kids can work at it. The tracks can stay set-up and they can vary the cars, and then it's not all over your family room.
Save the manufacturer's information and particularly the parts list - many times you can order a missing part from them, particularly if it is key to the toy's operation.
The kids can learn to sort parts for the things you already have. Make a game of it, not a chore. If you REALLY want to be organized, you can stick paper labels (like the circular ones for garage sales) or even a dot of nail polish (if you have a lot of colors) on the bottom of toys - one color for every set. Then the kids (and you) can sort all the red things into one tote, the pink dots into another, and so on.
For Legos, you can throw them all into one tote, or you can sort them by type (if for a specific set like one of those Star Wars things or the moonscapes) or just separate them randomly into gallon sized ziploc bags, and just let the kids take out one bag apiece. When done, they can push all the pieces into one clear bag, or you can use a dustpan or a beach shovel to scoop them up and slide them into the bag when it's on its side!!
It CAN be done - you just have to start out right! And don't bother trying to convince MIL to change her ways - it ain't gonna work! But she's more than welcome to come on over and sit on the floor with the kids to play this stuff with them! In fact, I think you should PLAN on a monthly play date and let her experience the same "joy" you are experiencing! Just smile sweetly and say "Now, isn't this as much fun as you thought?"