Just about all toolboxes have tote trays. Tote trays keep smaller tools and parts separate from larger ones. If a large percentage of your tool set is made up of smaller tools and pieces, perhaps it's time to look into getting a multi-drawer tool chest. Slightly larger than a toolbox, it allows you to divide and organize small tools into groups that can be quickly located, collected, and returned.
Instead of putting a paint smear across the outside of a can to mark the level of paint left inside (which can be messy and obliterate the label), use a rubber band instead. Put it around the can and roll it down to the level of the paint. Just by glancing at the rubber band, which is visible all the way around, you will know how much paint is left.