Craig,
I have the same problem with my LandCruiser wagon. I have more room than you so I am able to use a rubbermaid rough-tote box to hold my goodies. They do have some smaller boxes that may work for you.
Otherwise I'd do some web searching for storage boxes/bags for SUVs. You may find someone has already solved your problem and is just waiting to sell you the solution.
An important issue is how you will secure the load. In an accident you do not want a large box full of tools and food hitting you in the back of the head. Same goes for the the lid. If a lid pops loose it won't matter if you have secured the box.
For my Cruiser I drilled some holes in the side of the box (two in each corner) and use 4 heavy duty zip-ties to secure the box to the side of the cruiser cargo area (there are two metal bars behind the side panel). The zip-ties can be cut and replaced easily if the box needs to be removed. The lid has handles that can be locked. You can use pad locks or just use a dog leash type latch to secure the handles. I also have a heavy duty pet type guard in the cargo area to keep any other items in the rear (groceries, etc) from hitting me in the noggin' if I brake fast.
Whether you go with hard side or soft side cargo holder make sure you have secured the holder and any lids or flaps.
Another trick: Pull the side panels off in the cargo area and see where you can stash some items. My wife has a 2004 Taurus wagon. We use the foot well in the rear to keep a BOB, bottled water, and a blanket. Out of sight and secure under the locked hinged cover. I pulled off the side cover that holds the spare tire. I was able to stuff in a pair of gloves, ground tarp/space blanket, and can of fix-a-flat. If you dig around a bit you would be amazed where you can squirrel away many of those little used items that don't require instant access. Check under the hood. Sometimes you can fit a small water proof ammo box in a nook in the engine compartment. This is a great place to stash some tools. Forget about keeping the tools in nice organized boxes. I put the sockets in a ziplock to keep them together, the rest of the tools get put in till no more will fit. I was able to reduce the size of my too box just by removing any packaging or tool organizers. Just lay them in there till no more will fit. Check under seats for storage sites. For light items they can be put in rubbermaid/tupperware boxes with velcro on the bottom (hook side). The velcro grips the carpet and keeps the item from shifting while driving. The front seat kick panels might have a bit of room for some specialty item or tool that might me helpful in a pinch, but doesn't require instant access.
In summary:
Secure your load.
Don't feel like you have to put all items in one location. Get creative. Get a flashlight and screw driver and take a detailed tour of the inside to the Subaru and the engine compartment.
If you do distribute items around the vehicle, keep an inventory list in your glove box so you can find the items you need quickly without having to strip the car to get to that hidden crescent wrench or pocket VOM.
Good luck. TR