This is very probably suggested elsewhere but thought I'd share anyway just in case.
As you're adventuring around the world you can find different kinds of chest to pick up and you can send them to your camp. Not only do their icons sometimes look different in your bag/traveller's chest, but they are often named different things - so for example I've got two chests which look the same but one is called 'Moss Covered Chest' and the other 'Wooden Chest.'
But also you can find items that look like a single item but are actually proper containers. So for example, near the windmill in the Blighted Village, just as you hop down the step northward, there's a hole you can loot. Inside there's a book, and if you 'read' it, it turns out to be a container. I've also found a skeleton and an animal carcass that does this. Please let me know if there are others - I'd like to collect them!
So I've got all these different containers in my Traveller's Chest, and I use different ones to manage my inventory - so obviously books go in The Book Container, I use a spikey chest with cow skull 'Crude Chest' I found in the Goblin Camp for things I consider to be 'evil' or unpleasant, I've got a 'painted chest' for explosives, barrels and arrows, an 'adamantine' chest for gems and other valuables, etc etc. Point is I've found enough different types of container around the world to tell them apart easily.
And, if you open these containers from within your Traveller's Chest, you can select multiple items from the main body of the Traveller's Chest and drag them across to the container you have open. It is a bit fiddly though.
Anyway, I know this isn't perfect, but until there is a better solution, it's really helped me sort my stuff.
Sorry if I've sounded condescending or really 'obvious' but I hope it helps someone! Thanks for reading!