Soft bedcover with toolbox. Any ideas on modification?

I have a '93 Toyota Pickup, standard cab, standard bed, manual 5 speed. A buddy gave me a soft cover for it (Sportmaster brand) that snaps onto four rails that go on the top of the bed and tailgate. However, I have a slim, low profile toolbox on the truck as well.

Any advice on how to modify the system to work with the toolbox?

My current plan is to cut the side rails to fit between the toolbox and the tailgate and also use the tailgate rail. I don't plan to use the short rail that goes next to the cab. I also don't plan to cut the cover, just to either tuck it down or find a way to attach it to the toolbox (possibly with velcro or paracord).

I'm open to all advice.