I am having some organizational problems. Specifically there are folders everywhere and I have no idea what is supposed to be where. I have three screenshots one of inside the content folder and one of inside /Documents/Studio3 which is where content folder is and one of inside Runtime. I think things installed wrong because there are weird duplicates, Daz can't find everything, and I want to know what needs merging, what needs moving, and what to leave alone. 

Can anyone help?

Unless you're using a fairly outdated machine, or are using some older tools that haven't been updated to work in DS4.6, I wouldn't be using DS3. DS4.6 will handle all of your older content (except for certain older tools, as I've already mentioned), and I personally find it much easier to use, customize, and organize than DS3 or even the newer versions of Poser. (Actually, I don't user Poser at all anymore: that outdated interface irks the hell out of me.)

DS3 is also not being updated anymore, while DS4 is (which is kind of a mixed blessing -- some updates are better than others, and some seem to add new issues -- the current version of DAZ Studio Pro 4.6 (4.6.3.52) seems to be a bit more touchy than the previous version).

Move all your folders labeled content to the one main one. And merge.

You should have a set up some thing like this

My documents/daz3/my library/content/inside content should be one of each, data, runtime, people, shaders, scenes, ect.

Hope this helps.

 Don't be too discouraged; content management is something that befuddles even the most experienced Daz User. It's been an issue almost since Day 1 and only gets worse as you acquire more content.

There is almost as many methods / suggestions as their are Daz users. I would suggest experimenting with each suggestion (with the expectation of having to delete and try something else) until you find an organizational method that works for you.

Personally I have tried these tactics:

1. Organize by type (people, props, etc.). Each in their own Runtime.
2. Organize by product age. Older items might not be as important to you.
3. Install only the items that I know I need on a regular basis (people, lights, shaders). Then install others as needed for each project and uninstall when done.