There are SO many methods of inventory management. The most important thing is to find what works best for you. I personally use folders/subfolders. Some of my friends prefer storage boxes. I even have one friend that has a RL notebook with everything written down.
I prefer folders and subfolders to boxes simply because I may not always be in a good place to take out a box if I have a sudden urge to use an item. With the folders method I have easy access to everything in my inventory. The main disadvantage is that this method does not reduce inventory count like storage boxes do.
As far as categorizing... As one poster mentioned you really just have to figure out how you process information. For me, clothing is easy. Divided into formal, dress clothes, casual and full outfits (for those outfits I don't wish to separate). Then subdivided into shirts, pants... etc. Objects are where things can really become a mess. I do a lot of sim designing and some building so I tend to categorize mine that way. In the case of hunts you are going to end up with a lot of random objects so you will have to look at what you have to find the best way to divide them (vehicles, weapons, furniture, etc.).
If you still aren't sure on methods there's an in world group, Builders Brewery that offers several classes on inventory management. You could look them up and attend some of those.