At the moment, I am mostly using RealmWorks. I'm also using OneNote for timeline tracking while I desperately await the calendar function to be cleaned up and implemented.
As far as organising your existing notes, in almost all cases RW will be just a bit different to anything you use right now, but it's extraordinarily well thought out.
High level overview (subject to change, beta product, etc, etc):
Categories: moderately broad groups of topics that are of the same overall type. Examples include Individuals, Communities, Groups. The included Categories in the software will cover most of your needs, but you may need to create custom Categories for your specific needs.
Topics: specific entries. Every character is a topic, every city is a topic, every organisation, kingdom, god, magic item, planet, plane of existence, etc... they're all topics. If it has a name, it's a topic.
Snippets: individual pieces of information about a particular topic. If you're like me, you won't be used to separating information into these discrete little chunks, but it's well worth the effort. Just looking at a single person, you'll have snippets for: Date of birth, place of birth, place of residence, friends, family, foes, beliefs, likes, dislikes, job, history, personality, appearance, race, gender, pictures, and many more. As many more as you want.
Your biggest task will be to create all of your topics. I would recommend starting big, and working your way down. Planes of existence, or planets, or galactic quadrants, or whatever the largest-scale regions of your campaign are. Then move to tighter and tighter scales. There are really two reasons I suggest this. Firstly, so that you have a definite input plan and can see your progress starting to shape up quickly, but secondly (and perhaps more importantly) because when you create smaller-scale topics you will want to use the larger scale ones as Containers (topics which are made up of numerous other topics), and having the larger topics already in place means it's easy to get into the habit of assigning the Container as you're going along.
If you already have your campaign notes in electronic form, you've already won half the battle, though, since copy/pasting information and breaking it up into snippets is utterly trivial.
And I haven't even touched on plots.