I use the OEM jacks, so those stash well in the designated places.
Although I don't have a hydraulic jack in my trunk, whenever I'm transporting rigid or heavy objects that might move around, I put them in a strong box, a milk crate or one of the cheap duffel bags I have gotten from goodwill.
Not a one-size-fits-all by any means, but I find that unless I'm driving like Ken Block, these tend to stay planted better than having something rolling around untethered in the trunk, especially something with wheels.
Now here's the wild side:
If your trunk sees a lot of utility and you don't think the OEM accessory organizer is up to the task, you might consider a variation of what I did to secure my subwoofer in a previous vehicle.
I bought some sturdy plywood from Lowe's and traced the trunk mat over it. Then I sawed along the line, making it a little smaller than the template, and made it in 2 pieces so that I could incorporate a hinge to access the spare tire and OEM jacking tools. Plus I think it wouldn't get in the trunk as one piece anyway,
Put the trunk mat away to save it, or keep using it if you please, and you can screw some strips of wood down to box permanent stuff in... or you can build something with taller sides to keep your jack from rolling around.