|Ok so this might be a bit contra the "one bag" idea but I like to think of this suggestion as pockets instead of bags. I love the mod but it can be a bit hard to keep things organized. My suggestion is that you allow people to create custom subsections or "pockets". This would work the same way as Bag Break works now (but at user set places) with the addition of a label. You give a name and a size and a pocket (subsection) is created. Unsectioned space is simply left as it is now.
Here's a picture of what I'm suggesting. This picture contains three custom pockets names "Quest Items", "Usables" and "Gear". They are set to sizes 14, 12 and 12.