I saw this tip many years ago, but could not find its original author. So, credits to who ever you are.
I took two pint size plastic oil containers (quart size fits the bigger fender bags) and cut the tops off. Put necessary tools in one half and slide the second half over the first. This works great as the edges are smooth and wont wear through the fender bag. The oil containers also help to keep parts at bay while doing a trail side repair. I am able to keep all the tools I wish to carry in the pint size ones so the quart sized ones, if they fit your bag, will hold a bunch more