I like paper but I also use the computer for most everything then print if I want it on paper. One app I really love and have used for years is PENZU. It is an online Journal. Love it. They offer a single journal for free but if you want multiple notebooks they charge 19 dollars a year. It's nice because it is accessible anywhere you have internet access.

For sorting out chapters and scenes I used to use Writers Cafe but recently switched to yWriter which is nice for organizing your scenes and chapters. You can move them around by dragging from one spot to another if you want.

I work on my novels at work, I am lucky I can do that. So, I scanned my notebook (listed below) and uploaded to Google Drive. That way I have it with me everywhere I go on my tablet. I write using pencil and paper when away from home then enter into Word when I get home.

Whenever I am starting a novel I set up a ring binder with tabs. I label the tabs
1. Outline,
I type my outline in the computer then print it out and put in my notebook. I like to scribble notes on it as I think of things.

2. Characters
I put all of my character profiles here. My current novel I have 20 characters which are families. I made out a visual map with the family names on top and each family member under the family name. I used VISIO for that and printed it out.

3. House Plans/Town drawings
I like to visual the houses my characters live in or work space. It helps with describing scenes. So I find house plans that suit my characters and print those out and put in here. I also find a place in Google I like, create a fictional name usually, and print it out with the streets etc.. Or I draw my own.

4. Research/Notes
This is where I keep notes and research I've done for my novel.

5. Timelines/Schedules
I make out charts of timelines and their daily schedules so that I can keep track of when and what with who and where.
Really helps a lot.