I moved my C12 into a sys 2 years ago. I just swapped the insert over. I throw everything else on top: Bits stay in the case they came in. Small level, tape measure, things like that... So many small jobs can be handled with just a drill and a few things, so the exatr room made sense.
My T15 always has a 4 drawer sortainer latched underneath to hold everything from kreg jig and screws to 10" bits, dowel centers, etc, etc. That rolls around the shop on top of the CT mini, and while yes, the sortainer's not the most spec efficient way to do things, it's faster and neater than pulling out trays.